SMTL ID : 5fjo.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.08 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, Q.26, R.29, M.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.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:F.19, A:F.19, A:T.21, A:F.23, A:Q.26, A:I.293 Hydrogen bonds: A:S.135, A:K.161, A:K.163, A:N.191, A:D.291, A:D.316 Water bridges: A:N.191, A:K.263, A:D.291 Salt bridges: A:K.161, A:K.163, A:K.263 NPQ.3: 19 residues within 4Å: Chain B: F.19, T.21, Q.26, R.29, M.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.4 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:F.19, B:F.19, B:T.21, B:Q.26, B:I.293 Hydrogen bonds: B:S.135, B:K.161, B:K.163, B:N.191, B:D.291 Water bridges: B:N.191, B:D.291, B:D.316 Salt bridges: B:K.161, B:K.163, B:K.263 NPQ.5: 20 residues within 4Å: Chain C: F.19, T.21, F.23, Q.26, R.29, M.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 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:F.19, C:F.19, C:T.21, C:F.23, C:Q.26, C:I.293 Hydrogen bonds: C:S.135, C:K.161, C:K.163, C:N.191, C:D.291, C:D.316 Water bridges: C:N.191, C:K.263, C:D.291 Salt bridges: C:K.161, C:K.163, C:K.263 NPQ.7: 19 residues within 4Å: Chain D: F.19, T.21, Q.26, R.29, M.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.8 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:F.19, D:F.19, D:T.21, D:Q.26, D:I.293 Hydrogen bonds: D:S.135, D:K.161, D:K.163, D:N.191, D:D.291 Water bridges: D:N.191, D:D.291, D:D.316 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, Q.26, R.29, M.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.10 18 PLIP interactions: 18 interactions with chain E Hydrophobic interactions: E:F.19, E:F.19, E:T.21, E:F.23, E:Q.26, E:I.293 Hydrogen bonds: E:S.135, E:K.161, E:K.163, E:N.191, E:D.291, E:D.316 Water bridges: E:N.191, E:K.263, E:D.291 Salt bridges: E:K.161, E:K.163, E:K.263 NPQ.11: 19 residues within 4Å: Chain F: F.19, T.21, Q.26, R.29, M.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.12 16 PLIP interactions: 16 interactions with chain F Hydrophobic interactions: F:F.19, F:F.19, F:T.21, F:Q.26, F:I.293 Hydrogen bonds: F:S.135, F:K.161, F:K.163, F:N.191, F:D.291 Water bridges: F:N.191, F:D.291, F:D.316 Salt bridges: F:K.161, F:K.163, F:K.263 NPQ.13: 20 residues within 4Å: Chain G: F.19, T.21, F.23, Q.26, R.29, M.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 18 PLIP interactions: 18 interactions with chain G Hydrophobic interactions: G:F.19, G:F.19, G:T.21, G:F.23, G:Q.26, G:I.293 Hydrogen bonds: G:S.135, G:K.161, G:K.163, G:N.191, G:D.291, G:D.316 Water bridges: G:N.191, G:K.263, G:D.291 Salt bridges: G:K.161, G:K.163, G:K.263 NPQ.15: 19 residues within 4Å: Chain H: F.19, T.21, Q.26, R.29, M.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.16 16 PLIP interactions: 16 interactions with chain H Hydrophobic interactions: H:F.19, H:F.19, H:T.21, H:Q.26, H:I.293 Hydrogen bonds: H:S.135, H:K.161, H:K.163, H:N.191, H:D.291 Water bridges: H:N.191, H:D.291, H:D.316 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 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:D.189, A:E.214, A:D.239, NPQ.1, H2O.12 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.29 MG.6: 7 residues within 4Å: Chain C: K.161, D.189, N.191, E.214, D.239, K.263 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.46 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.63 MG.10: 7 residues within 4Å: Chain E: K.161, D.189, N.191, E.214, D.239, K.263 Ligands: NPQ.9 5 PLIP interactions: 3 interactions with chain E, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: E:D.189, E:E.214, E:D.239, NPQ.9, H2O.79 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.96 MG.14: 7 residues within 4Å: Chain G: K.161, D.189, N.191, E.214, D.239, K.263 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.113 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.130

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

N-succinylamino acid racemase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

N-succinylamino acid racemase

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