PDBe 5hd1

X-ray diffraction
2.7Å resolution

Crystal structure of antimicrobial peptide Pyrrhocoricin bound to the Thermus thermophilus 70S ribosome

Released:

Function and Biology Details

Structure analysis Details

Assemblies composition:
hetero 56-mer
hetero 55-mer (preferred)
Entry contents:
50 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (55 distinct):
Pyrrhocoricin Chains: 1z, 2z
Molecule details ›
Chains: 1z, 2z
Length: 20 amino acids
Theoretical weight: 2.34 KDa
Source organism: Pyrrhocoris apterus
Expression system: Not provided
UniProt:
  • Canonical: P37362 (Residues: 1-20; Coverage: 100%)
30S ribosomal protein S2 Chains: 1b, 2b
Molecule details ›
Chains: 1b, 2b
Length: 256 amino acids
Theoretical weight: 29.32 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80371 (Residues: 1-256; Coverage: 100%)
Gene names: TTHA0861, rps2, rpsB
Sequence domains: Ribosomal protein S2
30S ribosomal protein S3 Chains: 1c, 2c
Molecule details ›
Chains: 1c, 2c
Length: 239 amino acids
Theoretical weight: 26.75 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80372 (Residues: 1-239; Coverage: 100%)
Gene names: TTHA1686, rps3, rpsC
Sequence domains:
30S ribosomal protein S4 Chains: 1d, 2d
Molecule details ›
Chains: 1d, 2d
Length: 209 amino acids
Theoretical weight: 24.37 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80373 (Residues: 1-209; Coverage: 100%)
Gene names: TTHA1665, rps4, rpsD
Sequence domains:
30S ribosomal protein S5 Chains: 1e, 2e
Molecule details ›
Chains: 1e, 2e
Length: 162 amino acids
Theoretical weight: 17.58 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ5 (Residues: 1-162; Coverage: 100%)
Gene names: TTHA1675, rpsE
Sequence domains:
30S ribosomal protein S6 Chains: 1f, 2f
Molecule details ›
Chains: 1f, 2f
Length: 101 amino acids
Theoretical weight: 11.99 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLP8 (Residues: 1-101; Coverage: 100%)
Gene names: TTHA0245, rpsF
Sequence domains: Ribosomal protein S6
30S ribosomal protein S7 Chains: 1g, 2g
Molecule details ›
Chains: 1g, 2g
Length: 156 amino acids
Theoretical weight: 18.05 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P17291 (Residues: 1-156; Coverage: 100%)
Gene names: TTHA1696, rps7, rpsG
Sequence domains: Ribosomal protein S7p/S5e
30S ribosomal protein S8 Chains: 1h, 2h
Molecule details ›
Chains: 1h, 2h
Length: 138 amino acids
Theoretical weight: 15.87 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P0DOY9 (Residues: 1-138; Coverage: 100%)
Gene names: TTHA1678, rpsH
30S ribosomal protein S9 Chains: 1i, 2i
Molecule details ›
Chains: 1i, 2i
Length: 128 amino acids
Theoretical weight: 14.41 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80374 (Residues: 1-128; Coverage: 100%)
Gene names: TTHA1464, rps9, rpsI
Sequence domains: Ribosomal protein S9/S16
50S ribosomal protein L2 Chains: 1D, 2D
Molecule details ›
Chains: 1D, 2D
Length: 276 amino acids
Theoretical weight: 30.53 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60405 (Residues: 1-276; Coverage: 100%)
Gene names: TTHA1689, rplB
Sequence domains:
50S ribosomal protein L3 Chains: 1E, 2E
Molecule details ›
Chains: 1E, 2E
Length: 206 amino acids
Theoretical weight: 22.45 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN8 (Residues: 1-206; Coverage: 100%)
Gene names: TTHA1692, rplC
Sequence domains: Ribosomal protein L3
50S ribosomal protein L4 Chains: 1F, 2F
Molecule details ›
Chains: 1F, 2F
Length: 210 amino acids
Theoretical weight: 23.27 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN9 (Residues: 1-210; Coverage: 100%)
Gene names: TTHA1691, rplD
Sequence domains: Ribosomal protein L4/L1 family
50S ribosomal protein L5 Chains: 1G, 2G
Molecule details ›
Chains: 1G, 2G
Length: 182 amino acids
Theoretical weight: 21.06 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ0 (Residues: 1-182; Coverage: 100%)
Gene names: TTHA1680, rplE
Sequence domains:
50S ribosomal protein L6 Chains: 1H, 2H
Molecule details ›
Chains: 1H, 2H
Length: 180 amino acids
Theoretical weight: 19.57 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P0DOY8 (Residues: 1-180; Coverage: 100%)
Gene names: TTHA1677, rplF
50S ribosomal protein L9 Chains: 1I, 2I
Molecule details ›
Chains: 1I, 2I
Length: 148 amino acids
Theoretical weight: 16.42 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLQ1 (Residues: 1-148; Coverage: 100%)
Gene names: TTHA0242, rplI
Sequence domains:
30S ribosomal protein S10 Chains: 1j, 2j
Molecule details ›
Chains: 1j, 2j
Length: 105 amino acids
Theoretical weight: 11.95 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN7 (Residues: 1-105; Coverage: 100%)
Gene names: TTHA1693, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
30S ribosomal protein S11 Chains: 1k, 2k
Molecule details ›
Chains: 1k, 2k
Length: 129 amino acids
Theoretical weight: 13.74 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80376 (Residues: 1-129; Coverage: 100%)
Gene names: TTHA1666, rps11, rpsK
Sequence domains: Ribosomal protein S11
30S ribosomal protein S12 Chains: 1l, 2l
Molecule details ›
Chains: 1l, 2l
Length: 132 amino acids
Theoretical weight: 14.64 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN3 (Residues: 1-132; Coverage: 100%)
Gene names: TTHA1697, rpsL
Sequence domains: Ribosomal protein S12/S23
30S ribosomal protein S13 Chains: 1m, 2m
Molecule details ›
Chains: 1m, 2m
Length: 126 amino acids
Theoretical weight: 14.34 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80377 (Residues: 1-126; Coverage: 100%)
Gene names: TTHA1667, rps13, rpsM
Sequence domains: Ribosomal protein S13/S18
30S ribosomal protein S15 Chains: 1o, 2o
Molecule details ›
Chains: 1o, 2o
Length: 89 amino acids
Theoretical weight: 10.58 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJ76 (Residues: 1-89; Coverage: 100%)
Gene names: TTHA1138, rpsO
Sequence domains: Ribosomal protein S15
30S ribosomal protein S16 Chains: 1p, 2p
Molecule details ›
Chains: 1p, 2p
Length: 88 amino acids
Theoretical weight: 10.41 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJH3 (Residues: 1-88; Coverage: 100%)
Gene names: TTHA1035, rpsP
Sequence domains: Ribosomal protein S16
30S ribosomal protein S17 Chains: 1q, 2q
Molecule details ›
Chains: 1q, 2q
Length: 105 amino acids
Theoretical weight: 12.33 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: A0A0N0BLS5 (Residues: 1-105; Coverage: 100%)
Gene names: BVI061214_01029, rpsQ
Sequence domains: Ribosomal protein S17
30S ribosomal protein S18 Chains: 1r, 2r
Molecule details ›
Chains: 1r, 2r
Length: 88 amino acids
Theoretical weight: 10.26 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLQ0 (Residues: 1-88; Coverage: 100%)
Gene names: TTHA0243, rpsR
Sequence domains: Ribosomal protein S18
30S ribosomal protein S19 Chains: 1s, 2s
Molecule details ›
Chains: 1s, 2s
Length: 93 amino acids
Theoretical weight: 10.61 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP2 (Residues: 1-93; Coverage: 100%)
Gene names: TTHA1688, rpsS
Sequence domains: Ribosomal protein S19
30S ribosomal protein S20 Chains: 1t, 2t
Molecule details ›
Chains: 1t, 2t
Length: 106 amino acids
Theoretical weight: 11.74 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80380 (Residues: 1-106; Coverage: 100%)
Gene names: TTHA1397, rps20, rpsT
Sequence domains: Ribosomal protein S20
30S ribosomal protein Thx Chains: 1u, 2u
Molecule details ›
Chains: 1u, 2u
Length: 27 amino acids
Theoretical weight: 3.35 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SIH3 (Residues: 1-27; Coverage: 100%)
Gene names: TTHA1396, rpsU
Sequence domains: 30S ribosomal protein Thx
50S ribosomal protein L13 Chains: 1N, 2N
Molecule details ›
Chains: 1N, 2N
Length: 140 amino acids
Theoretical weight: 15.93 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60488 (Residues: 1-140; Coverage: 100%)
Gene names: TTHA1465, rplM
Sequence domains: Ribosomal protein L13
50S ribosomal protein L14 Chains: 1O, 2O
Molecule details ›
Chains: 1O, 2O
Length: 122 amino acids
Theoretical weight: 13.32 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP8 (Residues: 1-122; Coverage: 100%)
Gene names: TTHA1682, rplN
Sequence domains: Ribosomal protein L14p/L23e
50S ribosomal protein L15 Chains: 1P, 2P
Molecule details ›
Chains: 1P, 2P
Length: 150 amino acids
Theoretical weight: 16.32 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ7 (Residues: 1-150; Coverage: 100%)
Gene names: TTHA1673, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
50S ribosomal protein L16 Chains: 1Q, 2Q
Molecule details ›
Chains: 1Q, 2Q
Length: 141 amino acids
Theoretical weight: 15.99 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60489 (Residues: 1-141; Coverage: 100%)
Gene names: TTHA1685, rplP
Sequence domains: Ribosomal protein L16p/L10e
50S ribosomal protein L17 Chains: 1R, 2R
Molecule details ›
Chains: 1R, 2R
Length: 118 amino acids
Theoretical weight: 13.75 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q9Z9H5 (Residues: 1-118; Coverage: 100%)
Gene names: TTHA1663, rpl17, rplQ
Sequence domains: Ribosomal protein L17
50S ribosomal protein L18 Chains: 1S, 2S
Molecule details ›
Chains: 1S, 2S
Length: 112 amino acids
Theoretical weight: 12.64 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ4 (Residues: 1-112; Coverage: 100%)
Gene names: TTHA1676, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
50S ribosomal protein L19 Chains: 1T, 2T
Molecule details ›
Chains: 1T, 2T
Length: 146 amino acids
Theoretical weight: 17.19 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60490 (Residues: 1-146; Coverage: 100%)
Gene names: TTHA1031, rplS
Sequence domains: Ribosomal protein L19
50S ribosomal protein L20 Chains: 1U, 2U
Molecule details ›
Chains: 1U, 2U
Length: 118 amino acids
Theoretical weight: 13.78 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60491 (Residues: 1-118; Coverage: 100%)
Gene names: TTHA0553, rplT
Sequence domains: Ribosomal protein L20
50S ribosomal protein L21 Chains: 1V, 2V
Molecule details ›
Chains: 1V, 2V
Length: 101 amino acids
Theoretical weight: 11.07 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60492 (Residues: 1-101; Coverage: 100%)
Gene names: TTHA1783, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
50S ribosomal protein L22 Chains: 1W, 2W
Molecule details ›
Chains: 1W, 2W
Length: 113 amino acids
Theoretical weight: 12.81 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP3 (Residues: 1-113; Coverage: 100%)
Gene names: TTHA1687, rplV
Sequence domains: Ribosomal protein L22p/L17e
50S ribosomal protein L23 Chains: 1X, 2X
Molecule details ›
Chains: 1X, 2X
Length: 96 amino acids
Theoretical weight: 10.76 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP0 (Residues: 1-96; Coverage: 100%)
Gene names: TTHA1690, rplW
Sequence domains: Ribosomal protein L23
50S ribosomal protein L24 Chains: 1Y, 2Y
Molecule details ›
Chains: 1Y, 2Y
Length: 110 amino acids
Theoretical weight: 12.09 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP9 (Residues: 1-110; Coverage: 100%)
Gene names: TTHA1681, rplX
Sequence domains:
50S ribosomal protein L25 Chains: 1Z, 2Z
Molecule details ›
Chains: 1Z, 2Z
Length: 206 amino acids
Theoretical weight: 23.24 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHZ1 (Residues: 1-206; Coverage: 100%)
Gene names: TTHA1589, rpl25, rplY, rptL5
Sequence domains:
50S ribosomal protein L27 Chains: 10, 20
Molecule details ›
Chains: 10, 20
Length: 85 amino acids
Theoretical weight: 9.53 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60493 (Residues: 1-85; Coverage: 100%)
Gene names: TTHA1782, rpmA
Sequence domains: Ribosomal L27 protein
50S ribosomal protein L28 Chains: 11, 21
Molecule details ›
Chains: 11, 21
Length: 98 amino acids
Theoretical weight: 11 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60494 (Residues: 1-98; Coverage: 100%)
Gene names: TTHA0042, rpmB
Sequence domains: Ribosomal L28 family
50S ribosomal protein L29 Chains: 12, 22
Molecule details ›
Chains: 12, 22
Length: 72 amino acids
Theoretical weight: 8.67 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP6 (Residues: 1-72; Coverage: 100%)
Gene names: TTHA1684, rpmC
Sequence domains: Ribosomal L29 protein
50S ribosomal protein L30 Chains: 13, 23
Molecule details ›
Chains: 13, 23
Length: 60 amino acids
Theoretical weight: 6.8 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ6 (Residues: 1-60; Coverage: 100%)
Gene names: TTHA1674, rpmD
Sequence domains: Ribosomal protein L30p/L7e
50S ribosomal protein L31 Chains: 14, 24
Molecule details ›
Chains: 14, 24
Length: 71 amino acids
Theoretical weight: 8.3 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJE1 (Residues: 1-71; Coverage: 100%)
Gene names: TTHA1073, rpmE
Sequence domains: Ribosomal protein L31
50S ribosomal protein L32 Chains: 15, 25
Molecule details ›
Chains: 15, 25
Length: 60 amino acids
Theoretical weight: 6.72 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80339 (Residues: 1-60; Coverage: 100%)
Gene names: TTHA0418, rpl32, rpmF
Sequence domains: Ribosomal L32p protein family
50S ribosomal protein L33 Chains: 16, 26
Molecule details ›
Chains: 16, 26
Length: 54 amino acids
Theoretical weight: 6.63 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P35871 (Residues: 1-54; Coverage: 100%)
Gene names: TTHA0250, rpl33, rpmG
Sequence domains: Ribosomal protein L33
50S ribosomal protein L34 Chains: 17, 27
Molecule details ›
Chains: 17, 27
Length: 49 amino acids
Theoretical weight: 6.13 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80340 (Residues: 1-49; Coverage: 100%)
Gene names: TTHA0446, rpl34, rpmH
Sequence domains: Ribosomal protein L34
50S ribosomal protein L35 Chains: 18, 28
Molecule details ›
Chains: 18, 28
Length: 65 amino acids
Theoretical weight: 7.51 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SKU1 (Residues: 1-65; Coverage: 100%)
Gene names: TTHA0552, rpmI
Sequence domains: Ribosomal protein L35
50S ribosomal protein L36 Chains: 19, 29
Molecule details ›
Chains: 19, 29
Length: 37 amino acids
Theoretical weight: 4.44 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHR2 (Residues: 1-37; Coverage: 100%)
Gene names: TTHA1668, rpmJ
Sequence domains: Ribosomal protein L36
30S ribosomal protein S14 type Z Chains: 1n, 2n
Molecule details ›
Chains: 1n, 2n
Length: 61 amino acids
Theoretical weight: 7.16 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: A0A0N0BLP2 (Residues: 1-61; Coverage: 100%)
Gene names: BVI061214_01033, rpsN, rpsZ
Sequence domains: Ribosomal protein S14p/S29e
P-site tRNA Chains: 1x, 2x
Molecule details ›
Chains: 1x, 2x
Length: 77 nucleotides
Theoretical weight: 24.85 KDa
Sequence domains: tRNA
Messenger RNA Chains: 1v, 2v
Molecule details ›
Chains: 1v, 2v
Length: 24 nucleotides
Theoretical weight: 7.8 KDa
5S ribosomal RNA Chains: 1B, 2B
Molecule details ›
Chains: 1B, 2B
Length: 121 nucleotides
Theoretical weight: 39.19 KDa
Sequence domains: 5S ribosomal RNA
16S ribosomal RNA Chains: 1a, 2a
Molecule details ›
Chains: 1a, 2a
Length: 1521 nucleotides
Theoretical weight: 493.65 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
23S ribosomal RNA Chains: 1A, 2A
Molecule details ›
Chains: 1A, 2A
Length: 2915 nucleotides
Theoretical weight: 947.9 KDa
Sequence domains: Bacterial large subunit ribosomal RNA

Ligands and Environments

3 bound ligands:

4 modified residues:

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 210.009Å b: 450.125Å c: 622.841Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.222 0.22 0.272
Expression system: Not provided