SMTL ID : 2ihu.1

Carboxyethylarginine synthase from Streptomyces clavuligerus: putative reaction intermediate complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.463, N.490, T.492 Ligands: TP9.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.463, A:T.492, H2O.10 MG.6: 4 residues within 4Å: Chain B: D.463, N.490, T.492 Ligands: TP9.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.463, B:T.492, H2O.24 MG.10: 5 residues within 4Å: Chain C: D.463, N.490, T.492 Ligands: TP8.13, TP9.14 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.463, C:T.492, H2O.38 MG.15: 4 residues within 4Å: Chain D: D.463, N.490, T.492 Ligands: TP9.17 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.463, D:T.492, H2O.51

6 x K: POTASSIUM ION(Non-covalent)

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

4 x TP9: (3Z)-4-{[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]AMINO}-3-MERCAPTOPENT-3-EN-1-YL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

TP9.4: 29 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, V.34, G.35, E.57, T.80, P.83, G.84, N.87, Q.121 Ligands: MG.1, TAR.5 20 PLIP interactions: 17 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.438, A:F.438, A:N.493, A:I.496, B:V.33, 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:G.494, A:L.495, B:Q.121 Water bridges: A:D.463, A:D.463, A:F.466 pi-Stacking: A:F.438 TP9.8: 28 residues within 4Å: Chain A: V.33, V.34, G.35, E.57, T.80, P.83, G.84, N.87, Q.121 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.6 23 PLIP interactions: 18 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:F.438, B:F.438, B:N.493, B:I.496, A:V.33, A:T.80, A:P.83 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, A:Q.121 Water bridges: B:D.463, B:F.466, B:N.490, A:E.57 pi-Stacking: B:F.438 TP9.14: 28 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, G.35, E.57, T.80, P.83, G.84, N.87, Q.121 Ligands: MG.10, TP8.13 17 PLIP interactions: 13 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:F.438, C:I.496, D:T.80, D:P.83 Hydrogen bonds: C:F.412, C:F.413, C:F.438, C:G.462, C:G.464, C:G.465, C:G.494, C:L.495, D:Q.121 Water bridges: C:F.466, C:N.490, D:E.57 pi-Stacking: C:F.438 TP9.17: 29 residues within 4Å: Chain C: V.33, V.34, G.35, E.57, T.80, P.83, G.84, N.87, Q.121 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, TAR.18 22 PLIP interactions: 18 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:F.438, D:F.438, D:N.493, D:I.496, 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:G.494, D:L.495, D:Y.561, C:Q.121 Water bridges: D:D.463, D:F.466, D:N.490 pi-Stacking: D:F.438

2 x TAR: D(-)-TARTARIC ACID(Non-covalent)

TAR.5: 8 residues within 4Å: Chain A: Y.271, I.410, R.414, H.415, L.495 Chain B: H.120, Q.121 Ligands: TP9.4 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Y.271, A:Y.271, A:R.414, B:Q.121 Water bridges: A:G.411, A:Y.499, B:R.36 Salt bridges: A:R.414, A:H.415, B:H.120 TAR.18: 11 residues within 4Å: Chain C: R.36, H.120, Q.121 Chain D: Y.271, I.410, R.414, H.415, S.436, L.495, Y.499 Ligands: TP9.17 12 PLIP interactions: 8 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:R.414, D:S.436, D:Y.499, C:Q.121, C:Q.121 Water bridges: D:Y.251, D:Y.251, D:G.411, C:R.36 Salt bridges: D:R.414, D:H.415, C:H.120

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 4 residues within 4Å: Chain B: R.367, E.370, F.371, D.374 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.367 Water bridges: B:E.370, B:H.385

1 x TP8: 5-(2-{[HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-2-[(1Z)-1-HYDROXY-3-(PHOSPHONOOXY)PROP-1-EN-1-YL]-3-{[(4Z)-4-IMINO-2- METHYL-4,5-DIHYDROPYRIMIDIN-5-YL]METHYL}-4-METHYL-1,3-THIAZOL-3-IUM(Non-covalent)

TP8.13: 31 residues within 4Å: Chain C: I.410, G.411, F.412, F.413, R.414, 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.499, Y.561 Chain D: V.33, G.35, R.36, E.57, T.80, P.83, N.87, H.120, Q.121 Ligands: MG.10, TP9.14 28 PLIP interactions: 23 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:F.438, C:F.438, C:N.493, C:L.495, C:I.496, D:V.33, D:T.80 Hydrogen bonds: C:F.412, C:F.413, C:R.414, C:S.436, C:F.438, C:G.462, C:G.464, C:G.465, C:G.494, C:L.495, C:Y.499, D:Q.121 Water bridges: C:Y.271, C:Y.271, C:S.436, C:S.436, C:F.466, C:N.490, D:E.57 pi-Stacking: C:F.438 Salt bridges: D:H.120

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

2007-11-27

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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