SMTL ID : 2iht.1

Carboxyethylarginine synthase from Streptomyces clavuligerus: SeMet structure

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 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.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.463, A:T.492, H2O.8 MG.6: 4 residues within 4Å: Chain B: D.463, N.490, T.492 Ligands: TPP.9 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.463, B:T.492, H2O.30 MG.11: 4 residues within 4Å: Chain C: D.463, N.490, T.492 Ligands: TPP.14 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.463, C:T.492, H2O.46 MG.15: 4 residues within 4Å: Chain D: D.463, N.490, T.492 Ligands: TPP.18 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.463, D:T.492, H2O.62

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

SO4.2: 8 residues within 4Å: Chain A: Y.271, I.410, R.414, H.415, S.436, L.495 Chain B: H.120, Q.121 11 PLIP interactions: 4 interactions with chain B, 7 interactions with chain A Water bridges: B:Q.121, B:Q.121, B:Q.121, A:R.414 Salt bridges: B:H.120, A:R.414, A:H.415 Hydrogen bonds: A:Y.271, A:Y.271, A:S.436, A:S.436 SO4.3: 5 residues within 4Å: Chain A: N.490, N.560, Y.561, D.562, F.563 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.490, A:Y.561, A:D.562, A:D.562 Water bridges: A:T.492, A:T.492, A:E.497 Salt bridges: A:K.513 SO4.7: 7 residues within 4Å: Chain A: H.120, Q.121 Chain B: Y.271, I.410, R.414, H.415, L.495 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Y.271, B:S.436, B:S.436 Water bridges: B:Y.251, B:R.414, B:Y.499, B:Y.499, A:Q.121, 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 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.490, B:N.560, B:Y.561, B:D.562 Water bridges: B:N.490, B:N.490 Salt bridges: B:K.513 SO4.12: 8 residues within 4Å: Chain C: Y.271, I.410, R.414, H.415, S.436, L.495 Chain D: H.120, Q.121 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:Y.271, C:Y.271, C:S.436, C:S.436 Water bridges: C:R.414, D:Q.121, D:Q.121 Salt bridges: C:R.414, C:H.415, D:H.120 SO4.13: 4 residues within 4Å: Chain C: N.490, N.560, Y.561, D.562 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.560, C:Y.561, C:D.562 Water bridges: C:N.490, C:N.490, C:T.492 Salt bridges: C:K.513 SO4.16: 7 residues within 4Å: Chain C: H.120, Q.121 Chain D: Y.271, I.410, R.414, H.415, L.495 11 PLIP interactions: 8 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:Y.271, D:S.436, D:S.436 Water bridges: D:Y.251, D:D.301, D:R.414, C:Q.121, C:Q.121 Salt bridges: D:R.414, D:H.415, C:H.120 SO4.17: 4 residues within 4Å: Chain D: N.490, N.560, Y.561, D.562 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:N.490, D:N.560, D:Y.561, D:D.562 Water bridges: D:T.492, D:T.492, D:F.563 Salt bridges: D:K.513

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.4: 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 18 PLIP interactions: 3 interactions with chain B, 15 interactions with chain A Hydrophobic interactions: B:T.80, B:P.83, A:F.438, A:I.496 Water bridges: B:Q.121, A:D.463, A:D.463, A:F.466 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 pi-Stacking: A:F.438 TPP.9: 26 residues within 4Å: Chain A: V.33, 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 21 PLIP interactions: 17 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:F.438, B:I.496, 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:N.490, B:G.494, B:L.495, B:Y.561 Water bridges: B:D.463, B:F.466, B:N.490, A:E.57, A:Q.121 pi-Stacking: B:F.438 TPP.14: 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.11 21 PLIP interactions: 16 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:F.438, C:I.496, D:V.33, D:T.80, D:P.83 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:G.494, C:L.495 Water bridges: C:D.463, C:D.463, C:F.466, D:E.57, D:Q.121 pi-Stacking: C:F.438 TPP.18: 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 20 PLIP interactions: 17 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:F.438, D:I.496, 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:D.463, D:F.466, C:Q.121 pi-Stacking: D:F.438

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: E.370, F.371, D.374, H.385 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.370, A:E.370 GOL.10: 4 residues within 4Å: Chain B: E.370, F.371, D.374, H.385 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.370 Water bridges: B:R.367 GOL.19: 5 residues within 4Å: Chain D: E.370, F.371, D.374, Y.378, H.385 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.370, D:E.370, D:H.385 Water bridges: D:Y.378 GOL.20: 5 residues within 4Å: Chain B: P.191 Chain D: A.199, V.322, D.334, V.336 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:D.334 Water bridges: D:D.200, D:D.334, D:V.336, B:N.189, B:T.190, B:A.192

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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