SMTL ID : 1upa.1

CARBOXYETHYLARGININE SYNTHASE FROM STREPTOMYCES CLAVULIGERUS (SEMET STRUCTURE)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-tetramer

Ligands

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 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.2 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.438, 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.462, A:G.464, A:G.465, A:G.494, A:L.495 Water bridges: A:D.463, A:D.463, A:F.466 pi-Stacking: A:F.438 TPP.5: 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.6 19 PLIP interactions: 16 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.438, B:I.496, A:V.33, A:T.80 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 Water bridges: B:D.463, B:F.466, B:N.490, A:E.57 pi-Stacking: B:F.438 TPP.9: 26 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 Ligands: MG.10 21 PLIP interactions: 18 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:F.438, C:F.438, C:I.496, D:V.33, D:T.80 Hydrogen bonds: C:F.412, C:F.413, C:S.436, C:F.438, C:G.462, C:G.464, C:G.465, C:N.490, C:N.490, C:G.494, C:L.495 Water bridges: C:D.463, C:D.463, C:F.466, D:E.57 pi-Stacking: C:F.438 TPP.13: 27 residues within 4Å: Chain C: V.33, V.34, 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.14 19 PLIP interactions: 18 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.438, D:N.493, D:I.496, C:T.80 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:D.463, D:F.466 pi-Stacking: D:F.438

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.463, N.490, T.492 Ligands: TPP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.463, A:T.492, H2O.210 MG.6: 4 residues within 4Å: Chain B: D.463, N.490, T.492 Ligands: TPP.5 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.463, B:T.492, H2O.528 MG.10: 4 residues within 4Å: Chain C: D.463, N.490, T.492 Ligands: TPP.9 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.463, C:T.492, H2O.701 MG.14: 4 residues within 4Å: Chain D: D.463, N.490, T.492 Ligands: TPP.13 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.463, D:T.492, H2O.916

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 7 residues within 4Å: Chain A: Y.271, I.410, R.414, H.415, L.495 Chain B: H.120, Q.121 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.271, A:Y.271, A:S.436, A:S.436 Water bridges: A:R.414 Salt bridges: A:R.414, A:H.415, B:H.120 SO4.4: 5 residues within 4Å: Chain A: N.490, N.560, Y.561, D.562, F.563 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.490, A:N.560, A:Y.561, A:D.562 SO4.7: 7 residues within 4Å: Chain A: H.120, Q.121 Chain B: Y.271, I.410, R.414, H.415, L.495 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Y.271, B:S.436, B:S.436, B:Y.499 Water bridges: B:R.414, B:R.414, A:Q.121, A:Q.121 Salt bridges: B:R.414, B:H.415, A:H.120 SO4.8: 5 residues within 4Å: Chain B: N.490, N.560, Y.561, D.562, F.563 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.490, B:N.560, B:Y.561, B:D.562 Salt bridges: B:K.513 SO4.11: 9 residues within 4Å: Chain C: Y.271, I.410, R.414, H.415, S.436, L.495, Y.499 Chain D: H.120, Q.121 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Y.271, C:Y.271, C:S.436, C:S.436, C:Y.499 Water bridges: C:R.414 Salt bridges: C:R.414, C:H.415, D:H.120 SO4.12: 7 residues within 4Å: Chain C: N.490, E.497, K.513, N.560, Y.561, D.562, F.563 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.490, C:N.560, C:Y.561, C:D.562 Salt bridges: C:K.513 SO4.15: 7 residues within 4Å: Chain C: H.120, Q.121 Chain D: Y.271, I.410, R.414, H.415, L.495 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Y.271 Water bridges: D:D.301, D:R.414 Salt bridges: D:R.414, D:H.415, C:H.120 SO4.16: 4 residues within 4Å: Chain D: N.490, N.560, Y.561, D.562 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.490, D:N.560, D:Y.561, D:D.562 Salt bridges: D:K.513

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Caines, M.E.C. et al., Crystal Structure and Mechanistic Implications of N2-(2-Carboxyethyl)Arginine Synthase, the First Enzyme in the Clavulanic Acid Biosynthesis Pathway. J.Biol.Chem. (2004)

Release Date

2003-11-20

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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