SMTL ID : 5fjr.1

N-acyl amino acid racemase from Amycolatopsis sp. Ts-1-60: Q26A M50I G291D F323Y mutant in complex with N-acetyl napthylalanine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.44 Å

Oligo State

homo-octamer

Ligands

8 x NPQ: N-acetyl naphthylalanine(Non-covalent)

NPQ.1: 20 residues within 4Å: Chain A: F.19, T.21, F.23, A.26, R.29, I.50, Y.55, S.135, K.161, K.163, D.189, N.191, E.214, D.239, K.263, D.291, M.292, I.293, Y.323 Ligands: MG.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.19, A:F.23, A:A.26, A:R.29, A:I.50, A:D.291, A:I.293 Hydrogen bonds: A:S.135, A:K.161, A:K.163, A:K.163, A:N.191 Water bridges: A:K.161, A:D.316 Salt bridges: A:K.161, A:K.163, A:K.263 NPQ.3: 20 residues within 4Å: Chain B: F.19, F.23, A.26, R.29, I.50, Y.55, S.135, K.161, K.163, D.189, N.191, E.214, D.239, K.263, D.291, M.292, I.293, D.316, Y.323 Ligands: MG.4 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:F.19, B:F.23, B:A.26, B:R.29, B:I.50, B:D.291, B:I.293 Hydrogen bonds: B:S.135, B:K.161, B:K.163, B:N.191, B:D.316 Salt bridges: B:K.161, B:K.163, B:K.263 NPQ.5: 19 residues within 4Å: Chain C: F.19, T.21, F.23, R.29, I.50, S.135, K.161, K.163, D.189, N.191, E.214, D.239, K.263, D.291, M.292, I.293, D.316, Y.323 Ligands: MG.6 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:F.19, C:F.23, C:I.50, C:D.291, C:I.293 Hydrogen bonds: C:S.135, C:K.163, C:K.163, C:N.191, C:N.261, C:D.316 Water bridges: C:N.191 Salt bridges: C:K.161, C:K.163, C:K.263 NPQ.7: 17 residues within 4Å: Chain D: F.19, A.26, I.50, Y.55, S.135, K.161, K.163, D.189, N.191, E.214, D.239, K.263, D.291, M.292, I.293, D.316 Ligands: MG.8 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:F.19, D:F.19, D:A.26, D:I.50, D:D.291, D:I.293, D:I.293 Hydrogen bonds: D:S.135, D:K.161, D:K.163, D:K.163, D:N.191, D:D.316, D:D.316 Water bridges: D:N.191, D:N.261 Salt bridges: D:K.161, D:K.163, D:K.263 NPQ.9: 20 residues within 4Å: Chain E: F.19, T.21, F.23, A.26, R.29, I.50, Y.55, S.135, K.161, K.163, D.189, N.191, E.214, D.239, K.263, D.291, M.292, I.293, Y.323 Ligands: MG.10 17 PLIP interactions: 17 interactions with chain E Hydrophobic interactions: E:F.19, E:F.23, E:A.26, E:R.29, E:I.50, E:D.291, E:I.293 Hydrogen bonds: E:S.135, E:K.161, E:K.163, E:K.163, E:N.191 Water bridges: E:K.161, E:D.316 Salt bridges: E:K.161, E:K.163, E:K.263 NPQ.11: 20 residues within 4Å: Chain F: F.19, F.23, A.26, R.29, I.50, Y.55, S.135, K.161, K.163, D.189, N.191, E.214, D.239, K.263, D.291, M.292, I.293, D.316, Y.323 Ligands: MG.12 16 PLIP interactions: 16 interactions with chain F Hydrophobic interactions: F:F.19, F:F.23, F:A.26, F:R.29, F:I.50, F:D.291, F:I.293 Hydrogen bonds: F:S.135, F:K.161, F:K.163, F:N.191, F:D.316, F:D.316 Salt bridges: F:K.161, F:K.163, F:K.263 NPQ.13: 19 residues within 4Å: Chain G: F.19, T.21, F.23, R.29, I.50, S.135, K.161, K.163, D.189, N.191, E.214, D.239, K.263, D.291, M.292, I.293, D.316, Y.323 Ligands: MG.14 16 PLIP interactions: 16 interactions with chain G Hydrophobic interactions: G:F.19, G:F.23, G:I.50, G:D.291, G:I.293 Hydrogen bonds: G:S.135, G:K.163, G:K.163, G:N.191, G:N.261, G:D.316, G:D.316 Water bridges: G:N.191 Salt bridges: G:K.161, G:K.163, G:K.263 NPQ.15: 17 residues within 4Å: Chain H: F.19, A.26, I.50, Y.55, S.135, K.161, K.163, D.189, N.191, E.214, D.239, K.263, D.291, M.292, I.293, D.316 Ligands: MG.16 18 PLIP interactions: 18 interactions with chain H Hydrophobic interactions: H:F.19, H:F.19, H:A.26, H:I.50, H:D.291, H:I.293, H:I.293 Hydrogen bonds: H:S.135, H:K.161, H:K.163, H:K.163, H:N.191, H:D.316 Water bridges: H:N.191, H:N.261 Salt bridges: H:K.161, H:K.163, H:K.263

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: K.161, D.189, N.191, E.214, D.239, K.263 Ligands: NPQ.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.189, A:E.214, A:D.239, NPQ.1 MG.4: 6 residues within 4Å: Chain B: K.161, D.189, N.191, E.214, D.239 Ligands: NPQ.3 5 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:D.189, B:E.214, B:D.239, NPQ.3, H2O.13 MG.6: 6 residues within 4Å: Chain C: K.161, D.189, N.191, E.214, D.239 Ligands: NPQ.5 5 PLIP interactions: 3 interactions with chain C, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: C:D.189, C:E.214, C:D.239, NPQ.5, H2O.18 MG.8: 6 residues within 4Å: Chain D: K.161, D.189, N.191, E.214, D.239 Ligands: NPQ.7 5 PLIP interactions: 3 interactions with chain D, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: D:D.189, D:E.214, D:D.239, NPQ.7, H2O.22 MG.10: 7 residues within 4Å: Chain E: K.161, D.189, N.191, E.214, D.239, K.263 Ligands: NPQ.9 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Ligand interactions Metal complexes: E:D.189, E:E.214, E:D.239, NPQ.9 MG.12: 6 residues within 4Å: Chain F: K.161, D.189, N.191, E.214, D.239 Ligands: NPQ.11 5 PLIP interactions: 3 interactions with chain F, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: F:D.189, F:E.214, F:D.239, NPQ.11, H2O.37 MG.14: 6 residues within 4Å: Chain G: K.161, D.189, N.191, E.214, D.239 Ligands: NPQ.13 5 PLIP interactions: 3 interactions with chain G, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: G:D.189, G:E.214, G:D.239, NPQ.13, H2O.42 MG.16: 6 residues within 4Å: Chain H: K.161, D.189, N.191, E.214, D.239 Ligands: NPQ.15 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.189, H:E.214, H:D.239, H2O.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sanchez-Carron, G. et al., Structure of N-Acylamino Acid Racemase Mutants in Complex with Substrates. To be Published

Release Date

2016-11-16

Peptides

O-SUCCINYLBENZOATE SYNTHASE: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

O-SUCCINYLBENZOATE SYNTHASE

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