SMTL ID : 4bf5.1

Structure of broad spectrum racemase from Aeromonas hydrophila

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 13 residues within 4Å: Chain A: I.72, K.74, Y.78, V.120, R.173, M.202, H.204, N.244, S.245, R.260, P.261, G.262, G.263 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.72, A:K.74 Hydrogen bonds: A:K.74, A:K.74, A:R.173, A:S.245, A:R.260, A:R.260, A:R.260, A:G.262, A:G.263 Water bridges: A:N.244 Salt bridges: A:K.74 pi-Cation interactions: A:H.204 PLP.17: 15 residues within 4Å: Chain A: Y.300 Chain B: I.72, K.74, Y.78, V.120, R.173, N.174, M.202, H.204, N.244, S.245, R.260, P.261, G.262, G.263 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:K.74 Hydrogen bonds: B:K.74, B:R.173, B:R.173, B:S.245, B:R.260, B:R.260, B:R.260, B:G.262, B:G.263 Water bridges: B:H.204, B:E.208, B:E.208, B:N.244, B:N.244, B:N.244, B:F.246 pi-Stacking: B:H.204

23 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 5 residues within 4Å: Chain A: M.171, R.173, N.174, M.202, H.204 Ligand excluded by PLIP CL.3: 6 residues within 4Å: Chain A: Y.323, R.324, L.383, N.387, M.394, W.398 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: Y.332, K.339, V.340, P.341 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain A: K.59, K.68, I.69, I.94, P.95 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: K.214, V.251, P.252, D.253 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: R.109, T.114 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: Q.336, G.337, Q.373, G.374 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: A.126, E.129, Q.130 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: P.26, R.32 Chain B: P.26, R.32 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: P.161, T.197, V.199 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain A: K.359 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain A: Q.225 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain B: M.171, R.173, N.174, M.202, H.204 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain B: K.214, V.251, P.252, D.253 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain B: E.209, K.210, F.246 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain B: I.270, S.272 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain B: G.411, H.414, H.416 Ligands: NI.30 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain B: G.411, H.412 Ligand excluded by PLIP CL.26: 4 residues within 4Å: Chain B: K.68, I.69, I.94, P.95 Ligand excluded by PLIP CL.27: 4 residues within 4Å: Chain B: K.184, E.185, L.188, W.226 Ligand excluded by PLIP CL.28: 5 residues within 4Å: Chain B: Y.323, R.324, M.394, W.398 Ligands: GOL.32 Ligand excluded by PLIP CL.29: 4 residues within 4Å: Chain B: Q.336, G.337, Q.373, G.374 Ligand excluded by PLIP CL.31: 5 residues within 4Å: Chain B: K.68, P.95, C.96, R.116, M.258 Ligand excluded by PLIP

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 13 residues within 4Å: Chain A: A.22, P.23, S.101, N.102, E.103, R.119, R.121, E.127 Chain B: A.39, S.40, N.41, A.42, P.403 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:N.41, B:N.41, A:N.102, A:E.103, A:E.127 Water bridges: B:A.39 GOL.14: 8 residues within 4Å: Chain A: V.289, W.311, V.355, T.356, L.358, K.359, G.360, V.361 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.356, A:G.360, A:V.361, A:V.361 GOL.15: 8 residues within 4Å: Chain A: Y.332, L.334, K.339, E.375, A.376, E.377, K.379, D.382 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.332, A:E.375, A:E.377 Water bridges: A:Q.338 GOL.18: 10 residues within 4Å: Chain A: P.23, Y.24 Chain B: N.33, D.76, G.399, Y.400, T.401, N.402, P.403, K.404 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.33, B:D.76, B:N.402, B:K.404, B:K.404, A:Y.24, A:Y.24 GOL.19: 13 residues within 4Å: Chain A: A.39, S.40, N.41, A.42, P.403 Chain B: A.22, P.23, S.101, N.102, E.103, R.119, R.121, E.127 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:N.41, B:N.102, B:E.103, B:E.127, B:E.127 Water bridges: A:A.39 GOL.32: 12 residues within 4Å: Chain B: G.322, Y.323, R.324, R.325, A.326, N.329, L.383, Y.386, A.389, M.394, W.398 Ligands: CL.28 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.322, B:R.325, B:A.326, B:N.329 Water bridges: B:W.398 GOL.33: 3 residues within 4Å: Chain B: L.358, K.359, G.360 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.359, B:G.360

1 x NI: NICKEL (II) ION(Non-covalent)

NI.30: 4 residues within 4Å: Chain B: G.411, H.414, H.416 Ligands: CL.24 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.414, B:H.416

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Espaillat, A. et al., Structural Basis for the Broad Specificity of a New Family of Amino-Acid Racemases. Acta Crystallogr.,Sect.D (2014)

Release Date

2014-01-15

Peptides

ALANINE RACEMASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ALANINE RACEMASE