SMTL ID : 2ihv.1

Carboxyethylarginine synthase from Streptomyces clavuligerus: 5-guanidinovaleric acid complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.463, N.490, T.492, G.494 Ligands: TPP.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.463, A:T.492, H2O.3 MG.5: 4 residues within 4Å: Chain B: D.463, N.490, T.492 Ligands: TPP.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.463, B:T.492, H2O.13 MG.10: 4 residues within 4Å: Chain C: D.463, N.490, T.492 Ligands: TPP.13 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.463, C:T.492, H2O.25 MG.15: 4 residues within 4Å: Chain D: D.463, N.490, T.492 Ligands: TPP.17 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.463, D:T.492, H2O.35

6 x K: POTASSIUM ION(Non-covalent)

K.2: 3 residues within 4Å: Chain A: E.396, E.397, A.399 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.396, A:E.397, A:A.399 K.6: 3 residues within 4Å: Chain B: E.396, E.397, A.399 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.396, B:A.399 K.7: 4 residues within 4Å: Chain A: H.56, S.468 Chain B: H.56, S.468 No protein-ligand interaction detected (PLIP) K.11: 3 residues within 4Å: Chain C: E.396, E.397, A.399 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.396, C:A.399 K.12: 4 residues within 4Å: Chain C: H.56, S.468 Chain D: H.56, S.468 No protein-ligand interaction detected (PLIP) K.16: 3 residues within 4Å: Chain D: E.396, E.397, A.399 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.396, D:E.397, D:A.399

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.3: 26 residues within 4Å: Chain A: I.410, G.411, F.412, F.413, S.436, S.437, F.438, G.462, D.463, G.464, G.465, N.490, T.492, N.493, G.494, L.495, I.496, Y.561 Chain B: V.33, G.35, E.57, T.80, P.83, G.84, N.87 Ligands: MG.1 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.438, A:I.496, B:T.80 Hydrogen bonds: A:F.412, A:F.413, A:S.436, A:F.438, A:G.462, A:G.464, A:G.465, A:N.490, A:G.494, A:L.495 Water bridges: A:F.466, A:N.490 pi-Stacking: A:F.438 TPP.8: 27 residues within 4Å: Chain A: V.33, V.34, G.35, E.57, T.80, P.83, G.84, N.87 Chain B: I.410, G.411, F.412, F.413, S.436, S.437, F.438, G.462, D.463, G.464, G.465, N.490, T.492, N.493, G.494, L.495, I.496, Y.561 Ligands: MG.5 18 PLIP interactions: 3 interactions with chain A, 15 interactions with chain B Hydrophobic interactions: A:V.33, A:T.80, B:F.438 Water bridges: A:E.57, B:D.463, B:F.466, B:N.490 Hydrogen bonds: B:F.412, B:F.413, B:S.436, B:F.438, B:G.462, B:G.464, B:G.465, B:G.494, B:L.495, B:Y.561 pi-Stacking: B:F.438 TPP.13: 27 residues within 4Å: Chain C: I.410, G.411, F.412, F.413, S.436, S.437, F.438, G.462, D.463, G.464, G.465, N.490, T.492, N.493, G.494, L.495, I.496, Y.561 Chain D: V.33, V.34, G.35, E.57, T.80, P.83, G.84, N.87 Ligands: MG.10 18 PLIP interactions: 5 interactions with chain D, 13 interactions with chain C Hydrophobic interactions: D:V.33, D:T.80, D:P.83, C:F.438 Water bridges: D:E.57, D:Q.121, C:F.466, C:N.490 Hydrogen bonds: C:F.412, C:F.413, C:S.436, C:F.438, C:G.462, C:G.464, C:G.465, C:G.494, C:L.495 pi-Stacking: C:F.438 TPP.17: 26 residues within 4Å: Chain C: V.33, G.35, E.57, T.80, P.83, G.84, N.87 Chain D: I.410, G.411, F.412, F.413, S.436, S.437, F.438, G.462, D.463, G.464, G.465, N.490, T.492, N.493, G.494, L.495, I.496, Y.561 Ligands: MG.15 19 PLIP interactions: 16 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:F.438, C:V.33, C:T.80, C:P.83 Hydrogen bonds: D:F.412, D:F.413, D:S.436, D:F.438, D:G.462, D:G.464, D:G.465, D:N.490, D:G.494, D:L.495, D:Y.561 Water bridges: D:D.463, D:F.466, D:N.490 pi-Stacking: D:F.438

4 x GVA: 5-{[AMINO(IMINO)METHYL]AMINO}PENTANOIC ACID(Non-covalent)

GVA.4: 14 residues within 4Å: Chain A: Y.271, D.301, R.303, M.306, I.410, R.414, H.415, L.495, Y.499, L.571, I.573 Chain B: R.36, H.120, Q.121 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Y.271, A:Y.271, A:L.571 Water bridges: A:R.414, A:R.414, A:Y.499, A:A.570, A:L.571 Salt bridges: A:D.301, A:R.414, A:H.415 GVA.9: 13 residues within 4Å: Chain A: H.120, Q.121 Chain B: Y.271, D.301, R.303, M.306, I.410, R.414, H.415, L.495, Y.499, L.571, I.573 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:Y.271, B:R.303, B:L.571 Water bridges: B:R.303, B:R.414, B:R.414, B:L.571 Salt bridges: B:D.301, B:R.414, B:H.415 GVA.14: 9 residues within 4Å: Chain C: Y.271, D.301, R.303, R.414, S.436, Y.499 Chain D: R.36, H.120, Q.121 9 PLIP interactions: 2 interactions with chain D, 7 interactions with chain C Water bridges: D:H.120, C:R.414 Salt bridges: D:H.120, C:D.301, C:R.414 Hydrogen bonds: C:Y.271, C:Y.271, C:R.303, C:S.436 GVA.18: 13 residues within 4Å: Chain C: H.120, Q.121 Chain D: Y.271, D.301, R.303, M.306, I.410, R.414, H.415, S.436, L.495, L.571, I.573 13 PLIP interactions: 1 interactions with chain C, 12 interactions with chain D Water bridges: C:R.36, D:Y.251, D:R.414, D:R.414, D:Y.499, D:Y.499, D:L.571 Hydrophobic interactions: D:Y.271 Hydrogen bonds: D:Y.271, D:L.571 Salt bridges: D:D.301, D:R.414, D:H.415

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Caines, M.E. et al., Structural and mechanistic studies on N(2)-(2-carboxyethyl)arginine synthase. Biochem.Biophys.Res.Commun. (2009)

Release Date

2007-09-18

Peptides

Carboxyethylarginine synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Carboxyethylarginine synthase

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