› 7nbd

X-ray diffraction
1.86Å resolution

Crystal structure of human serine racemase in complex with DSiP fragment Z235449082, XChem fragment screen.

Released:
DOI: 10.2210/pdb7nbd/pdb
PDB entry 7nbd coloured by chain, front view.
PDB entry 7nbd coloured by chain, side view.
PDB entry 7nbd coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Tyrosine 121 moves revealing a ligandable pocket that couples catalysis to ATP-binding in serine racemase.
Koulouris CR, Gardiner SE, Harris TK, Elvers KT, Mark Roe S, Gillespie JA, Ward SE, Grubisha O, Nicholls RA, Atack JR, Bax BD
Commun Biol 5 346 (2022)
PMID: 35410329

Function and Biology Details

Reactions catalysed: 
(1a) L-serine = 2-aminoprop-2-enoate + H(2)O
(1a) D-serine = 2-aminoprop-2-enoate + H(2)O
L-serine = D-serine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-190449 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Serine racemase Chains: AAA, BBB, CCC, DDD
Molecule details ›
Chains: AAA, BBB, CCC, DDD
Length: 346 amino acids
Theoretical weight: 37.46 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9GZT4 (Residues: 1-340; Coverage: 100%)
Gene name: SRR
Sequence domains: Pyridoxal-phosphate dependent enzyme

Ligands and Environments


Cofactor: Ligand PLP 4 x PLP
7 bound ligands:
Ligand GOL 8 x GOL
Ligand CA 7 x CA
Ligand MG 2 x MG
Ligand JFS 2 x JFS
Ligand EDO 3 x EDO
Ligand PGE 1 x PGE
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P21
Unit cell:
a: 48.012Å b: 154.846Å c: 85.451Å
α: 90° β: 98.043° γ: 90°
R-values:
R R work R free
0.178 0.176 0.207
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 mentions without citation

Vps27 recruits ESCRT machinery to endosomes during MVB sorting.
Katzmann et al. (2003)
1 more