4iyd

X-ray diffraction
1.66Å resolution

Insulin glargine crystal structure 1

Released:
Source organism: Homo sapiens
Entry authors: Barba de la Rosa AP, Lara-Gonzalez S, Montero-Moran GM, Escobedo-Moratilla A

Function and Biology Details

Reactions catalysed:
4 sulfur + 4 H(2)O + O(2) = 2 H(2)S + 2 HSO(3)(-) + 2 H(+)
Release of an N-terminal pyroglutamyl group from a polypeptide, the second amino acid generally not being Pro.
Formate + NAD(+) = CO(2) + NADH
AMP + diphosphate = adenine + 5-phospho-alpha-D-ribose 1-diphosphate
Prephenate + NADP(+) = 4-hydroxyphenylpyruvate + CO(2) + NADPH
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin
4 Fe(2+) + 4 H(+) + O(2) = 4 Fe(3+) + 2 H(2)O
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
N-substituted aminoacyl-tRNA + H(2)O = N-substituted amino acid + tRNA
L-asparagine + H(2)O = L-aspartate + NH(3)
Selective hydrolysis of -Xaa-Xaa-|-Yaa- bonds in which each of the Xaa can be either Arg or Lys and Yaa can be either Ser or Ala.
Hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)- glycosidic linkages of terminal sialic acid residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.
Hydrolysis of (1->4)-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins
NADH + ROOH + H(+) = NAD(+) + H(2)O + ROH
Nitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+)
Endopeptidase with a preference for cleavage when the P1 position is occupied by Glu-|- and the P1' position is occupied by Gly-|-
NTP + H(2)O = NDP + phosphate
ATP + H(2)O + 4 H(+)(Side 1) = ADP + phosphate + 4 H(+)(Side 2)
A (3R)-3-hydroxyacyl-[acyl-carrier protein] = a trans-2-enoyl-[acyl-carrier protein] + H(2)O
ATP + pyruvate = ADP + phosphoenolpyruvate
ATP + acetate + CoA = AMP + diphosphate + acetyl-CoA
Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus.
ATP + (R)-5-diphosphomevalonate = ADP + phosphate + isopentenyl diphosphate + CO(2)
A beta-lactam + H(2)O = a substituted beta-amino acid
Hydrolysis of (1->4)-beta-D-glucosidic linkages in beta-D-glucans containing (1->3)- and (1->4)-bonds
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Acetyl-CoA + L-2,4-diaminobutanoate = CoA + N(4)-acetyl-L-2,4-diaminobutanoate
L-glutamate 5-semialdehyde + NAD(+) + H(2)O = L-glutamate + NADH
L-histidinol + H(2)O + 2 NAD(+) = L-histidine + 2 NADH
Maleate = fumarate
2 H(2)O(2) = O(2) + 2 H(2)O
Endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans
Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more (1->4)-alpha-linked D-glucose units
(S)-malate + NAD(+) = oxaloacetate + NADH
D-glyceraldehyde 3-phosphate + phosphate + NAD(+) = 3-phospho-D-glyceroyl phosphate + NADH
2 superoxide + 2 H(+) = O(2) + H(2)O(2)
N,N-dimethylformamide + H(2)O = dimethylamine + formate
Beta-nicotinate D-ribonucleotide + 5,6-dimethylbenzimidazole = nicotinate + alpha-ribazole 5'-phosphate
A glutathione-S-conjugate + H(2)O = an (L-cysteinylglycine)-S-conjugate + L-glutamate
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
UDP-N-acetyl-alpha-D-mannosamine + N-acetyl-alpha-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol = UDP + N-acetyl-beta-D-mannosaminyl-(1->4)-N-acetyl-alpha-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol
Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.
Hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides
ATP + pyridoxal = ADP + pyridoxal 5'-phosphate
Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
Selective cleavage of Tyr-|-Gly bond in picornavirus polyprotein.
An aliphatic amide = a nitrile + H(2)O
Hydrolysis of terminal, non-reducing (1->4)-linked alpha-D-glucose residues with release of alpha-D-glucose
Hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides
O-phospho-L-homoserine + H(2)O = L-threonine + phosphate
ATP + H(2)O = ADP + phosphate
L-proline + NAD(P)(+) = 1-pyrroline-5-carboxylate + NAD(P)H
A 3-beta-hydroxy-Delta(5)-steroid + NAD(+) = a 3-oxo-Delta(5)-steroid + NADH
A (5-L-glutamyl)-peptide + an amino acid = a peptide + a 5-L-glutamyl amino acid
ATP + [DNA-directed RNA polymerase] = ADP + [DNA-directed RNA polymerase] phosphate
ATP + L-arginine = ADP + N(omega)-phospho-L-arginine
5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + NADPH
ATP + kanamycin = ADP + kanamycin 3'-phosphate
1-(5-phospho-beta-D-ribosyl)-5-((5-phospho-beta-D-ribosylamino)methylideneamino)imidazole-4-carboxamide = 5-((5-phospho-1-deoxy-D-ribulos-1-ylamino)methylideneamino)-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide
ATP + D-ribose = ADP + D-ribose 5-phosphate
Orotidine 5'-phosphate + diphosphate = orotate + 5-phospho-alpha-D-ribose 1-diphosphate
ATP + a protein = ADP + a phosphoprotein
Chloride + O(2) = chlorite
(S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate = fumarate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide
A pyrimidine 5'-nucleotide + H(2)O = D-ribose 5-phosphate + a pyrimidine base
RH + [reduced NADPH--hemoprotein reductase] + O(2) = ROH + [oxidized NADPH--hemoprotein reductase] + H(2)O
Cyclic pyranopterin phosphate + 2 [molybdopterin-synthase sulfur-carrier protein]-Gly-NH-CH(2)-C(O)SH + H(2)O = molybdopterin + 2 [molybdopterin-synthase sulfur-carrier protein]
S-adenosyl 3-(methylthio)propylamine + putrescine = 5'-S-methyl-5'-thioadenosine + spermidine
ATP + L-methionine + H(2)O = phosphate + diphosphate + S-adenosyl-L-methionine
Cleavage of peptide bonds with very broad specificity.
Carbamoyl phosphate + L-aspartate = phosphate + N-carbamoyl-L-aspartate
(1a) ATP + (R)-lipoate = lipoyl-AMP + diphosphate
L-lysine + NADPH + O(2) = N(6)-hydroxy-L-lysine + NADP(+) + H(2)O
2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde
4 benzenediol + O(2) = 4 benzosemiquinone + 2 H(2)O
Chorismate = prephenate
Urea + H(2)O = CO(2) + 2 NH(3)
L-serine + L-homocysteine = L-cystathionine + H(2)O
Triacylglycerol + H(2)O = diacylglycerol + a carboxylate
A carboxylic ester + H(2)O = an alcohol + a carboxylate
L-alanine = D-alanine
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
CoA-(4'-phosphopantetheine) + apo-[acyl-carrier-protein] = adenosine 3',5'-bisphosphate + holo-[acyl-carrier-protein]
ATP + [biotin carboxyl-carrier protein]-biotin-N(6)-L-lysine + hydrogencarbonate- = ADP + phosphate + [biotin carboxyl-carrier protein]-carboxybiotin-N(6)-L-lysine
Protein N(6)-(dihydrolipoyl)lysine + NAD(+) = protein N(6)-(lipoyl)lysine + NADH
2 glutathione + ROOH = glutathione disulfide + H(2)O + ROH
An acyl-[acyl-carrier protein] + NADP(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADPH
ATP + deamido-NAD(+) + NH(3) = AMP + diphosphate + NAD(+)
Orotidine 5'-phosphate = UMP + CO(2)
A (Z)-hexadec-9-enoyl-[acyl-carrier protein] + a malonyl-[acyl-carrier protein] = a (Z)-3-oxooctadec-11-enoyl-[acyl-carrier protein] + CO(2) + an [acyl-carrier protein]
Tetradecanoyl-CoA + an N-terminal-glycyl-[protein] = CoA + an N-terminal-N-tetradecanoylglycyl-[protein]
An acyl-[acyl-carrier protein] + NAD(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH
Hydrolyzes glutaminyl bonds, and activity is further restricted by preferences for the amino acids in P6 - P1' that vary with the species of potyvirus, e.g. Glu-Xaa-Xaa-Tyr-Xaa-Gln-|-(Ser or Gly) for the enzyme from tobacco etch virus. The natural substrate is the viral polyprotein, but other proteins and oligopeptides containing the appropriate consensus sequence are also cleaved.
(R)-10-hydroxystearate = oleate + H(2)O
5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole = 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate
S-adenosyl-L-methionine + guanine(37) in tRNA = S-adenosyl-L-homocysteine + N(1)-methylguanine(37) in tRNA
(1a) ATP + [RNA ligase]-L-lysine = [RNA ligase]-N(6)-(5'-adenylyl)-L-lysine + diphosphate
(3R)-3-hydroxyacyl-[acyl-carrier-protein] + NADP(+) = 3-oxoacyl-[acyl-carrier-protein] + NADPH
A chalcone = a flavanone
(1a) isocitrate + NADP(+) = 2-oxalosuccinate + NADPH
N-acetyl-D-glucosamine 6-phosphate + H(2)O = D-glucosamine 6-phosphate + acetate
RX + glutathione = HX + R-S-glutathione
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
Hydrolyzes the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides
D-xylopyranose = D-xylulose
UTP + alpha-D-glucose 1-phosphate = diphosphate + UDP-glucose
Hydrolysis of proteins to small peptides in the presence of ATP and magnesium. Alpha-Casein is the usual test substrate. In the absence of ATP, only oligopeptides shorter than five residues are hydrolyzed (such as succinyl-Leu-Tyr-|-NHMec; and Leu-Tyr-Leu-|-Tyr-Trp, in which cleavage of the -Tyr-|-Leu- and -Tyr-|-Trp bonds also occurs).
D-fructose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde 3-phosphate
Hydrolysis of four peptide bonds in the viral precursor polyprotein, commonly with Asp or Glu in the P6 position, Cys or Thr in P1 and Ser or Ala in P1'.
Hydrolyzes a Gly-|-Gly bond at its own C-terminus, commonly in the sequence -Tyr-Xaa-Val-Gly-|-Gly, in the processing of the potyviral polyprotein.
Taurine + 2-oxoglutarate + O(2) = sulfite + aminoacetaldehyde + succinate + CO(2)
Peptidylproline (omega=180) = peptidylproline (omega=0)
Choline = trimethylamine + acetaldehyde
n UDP-alpha-D-glucose + 4-O-(poly((2R)-glycerophospho)-(2R)-glycerophospho)-N-acetyl-beta-D-mannosaminyl-(1->4)-N-acetyl-alpha-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol = n UDP + 4-O-(poly((2R)-2-alpha-D-glucosyl-1-glycerophospho)-(2R)-glycerophospho)-N-acetyl-beta-D-mannosaminyl-(1->4)-N-acetyl-alpha-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol
L-glutamate = D-glutamate
(R)-3-hydroxybutanoate + NAD(+) = acetoacetate + NADH
Endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans
(S)-3-hydroxyacyl-CoA + NAD(+) = 3-oxoacyl-CoA + NADH
H(2)CO(3) = CO(2) + H(2)O
Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-ribose 5-phosphate + D-xylulose 5-phosphate
(1a) L-glutamine + H(2)O = L-glutamate + NH(3)
Methylamine + H(2)O + 2 oxidized [amicyanin] = formaldehyde + NH(3) + 2 reduced [amicyanin]
Alpha-D-mannose 1-phosphate = D-mannose 6-phosphate
L-glutamate = 4-aminobutanoate + CO(2)
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
ADP + phosphate + acetyl-CoA + oxaloacetate = ATP + citrate + CoA
Hydrolyzes single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil
Anthranilate + N,N-dimethyl-1,4-phenylenediamine + 2 NAD(+) = 2-(4-dimethylaminophenyl)diazenylbenzoate + 2 NADH
L-arginine + 2-oxoglutarate + O(2) = (3S)-3-hydroxy-L-arginine + succinate + CO(2)
Reduced plastocyanin + oxidized ferredoxin + light = oxidized plastocyanin + reduced ferredoxin
Acetyl-CoA + H(2)O + oxaloacetate = citrate + CoA
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
Acetyl-CoA + a 2-deoxystreptamine antibiotic = CoA + N(3)-acetyl-2-deoxystreptamine antibiotic
Shikimate + NADP(+) = 3-dehydroshikimate + NADPH
ATP + AMP = 2 ADP
Hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides
ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
Release of any N-terminal amino acid, including proline, that is linked to proline, even from a dipeptide or tripeptide.
Methyl-CoM + CoB = CoM-S-S-CoB + methane
Cytosine + H(2)O = uracil + NH(3)
Beta-D-ribopyranose = beta-D-ribofuranose
ATP + glycerol = ADP + sn-glycerol 3-phosphate
(+)-trans-carveol + NAD(+) = (+)-(S)-carvone + NADH
GDP-beta-L-fucose + NADP(+) = GDP-4-dehydro-alpha-D-rhamnose + NADPH
Acetyl-CoA + L-serine = CoA + O-acetyl-L-serine
ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-tRNA(Lys)
Pyruvate + L-aspartate-4-semialdehyde = (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate + H(2)O
ATP + L-tryptophan + tRNA(Trp) = AMP + diphosphate + L-tryptophyl-tRNA(Trp)
Xylitol + NADP(+) = L-xylulose + NADPH
(3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H(2)O
ATP + gamma-L-glutamyl-L-cysteine + glycine = ADP + phosphate + glutathione
TSAVLQ-|-SGFRK-NH(2) and SGVTFQ-|-GKFKK the two peptides corresponding to the two self-cleavage sites of the SARS 3C-like proteinase are the two most reactive peptide substrates. The enzyme exhibits a strong preference for substrates containing Gln at P1 position and Leu at P2 position.
ATP + acetyl-CoA + HCO(3)(-) = ADP + phosphate + malonyl-CoA
Biochemical function:
Biological process:
  • not assigned
Cellular component:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Insulin A chain Chain: A
Molecule details ›
Chain: A
Length: 21 amino acids
Theoretical weight: 2.33 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P01308 (Residues: 90-109; Coverage: 23%)
Gene name: INS
Insulin B chain Chain: B
Molecule details ›
Chain: B
Length: 29 amino acids
Theoretical weight: 3.33 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P01308 (Residues: 25-53; Coverage: 34%)
Gene name: INS

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: I213
Unit cell:
a: 77.325Å b: 77.325Å c: 77.325Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.197 0.225
Expression system: Escherichia coli K-12