SMTL ID : 5wyf.1

Structure of amino acid racemase, 2.12 A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

homo-tetramer

Ligands

4 x ILP: N-[O-PHOSPHONO-PYRIDOXYL]-ISOLEUCINE(Non-covalent)

ILP.1: 21 residues within 4Å: Chain A: A.66, S.126, G.127, S.128, N.131, Y.154, H.155, G.156, E.229, D.234, D.262, V.264, N.265, K.292, R.420, W.462 Chain B: T.93, A.95, Y.96, F.320, T.321 22 PLIP interactions: 16 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:A.66, A:Y.154, A:V.264, A:N.265, A:W.462, B:A.95, B:Y.96 Hydrogen bonds: A:A.66, A:G.127, A:S.128, A:N.131, A:N.265, A:K.292, A:K.292, B:T.321, B:T.321 Water bridges: A:Y.154, A:D.234, B:N.125, B:T.322 Salt bridges: A:K.292, A:R.420 ILP.12: 21 residues within 4Å: Chain A: A.95, Y.96, L.319, F.320, T.321 Chain B: A.66, S.126, G.127, S.128, N.131, Y.154, H.155, G.156, E.229, D.234, D.262, V.264, N.265, K.292, R.420, W.462 22 PLIP interactions: 15 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:A.66, B:Y.154, B:N.265, B:W.462, A:A.95, A:Y.96, A:L.319 Hydrogen bonds: B:G.127, B:S.128, B:N.131, B:N.265, B:K.292, B:K.292, A:T.321, A:T.321 Water bridges: B:Y.154, B:D.234, A:N.125, A:T.322 Salt bridges: B:K.292, B:K.292, B:R.420 ILP.21: 18 residues within 4Å: Chain C: A.66, S.126, G.127, S.128, N.131, Y.154, H.155, E.229, D.234, D.262, V.264, N.265, K.292, R.420 Chain D: A.95, Y.96, F.320, T.321 22 PLIP interactions: 16 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:A.66, C:Y.154, C:V.264, C:N.265, D:A.95, D:Y.96 Hydrogen bonds: C:S.126, C:G.127, C:S.128, C:N.131, C:N.265, C:K.292, C:K.292, D:Y.96, D:Y.96, D:T.321 Water bridges: C:Y.154, C:E.229, D:T.322 Salt bridges: C:K.292, C:K.292, C:R.420 ILP.32: 21 residues within 4Å: Chain C: A.95, Y.96, L.319, F.320, T.321 Chain D: A.66, S.126, G.127, S.128, N.131, Y.154, H.155, G.156, E.229, D.234, D.262, V.264, N.265, K.292, R.420, W.462 21 PLIP interactions: 15 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:A.66, D:Y.154, D:V.264, D:N.265, D:W.462, C:A.95, C:Y.96, C:L.319 Hydrogen bonds: D:S.126, D:G.127, D:S.128, D:N.131, D:N.265, D:K.292, D:K.292, C:T.321 Salt bridges: D:K.292, D:K.292, D:R.420 Water bridges: C:N.125, C:T.322

36 x CD: CADMIUM ION(Non-covalent)

CD.2: 1 residues within 4Å: Chain A: D.17 Ligand excluded by PLIP CD.3: 1 residues within 4Å: Chain A: H.45 Ligand excluded by PLIP CD.4: 1 residues within 4Å: Chain A: H.47 Ligand excluded by PLIP CD.5: 1 residues within 4Å: Chain A: E.76 Ligand excluded by PLIP CD.6: 2 residues within 4Å: Chain A: H.200, E.243 Ligand excluded by PLIP CD.7: 1 residues within 4Å: Chain A: H.255 Ligand excluded by PLIP CD.8: 3 residues within 4Å: Chain A: R.365, H.366, E.447 Ligand excluded by PLIP CD.9: 2 residues within 4Å: Chain A: D.393, D.395 Ligand excluded by PLIP CD.10: 1 residues within 4Å: Chain A: H.407 Ligand excluded by PLIP CD.11: 2 residues within 4Å: Chain A: E.107 Chain B: E.25 Ligand excluded by PLIP CD.13: 2 residues within 4Å: Chain A: E.25 Chain B: E.107 Ligand excluded by PLIP CD.14: 1 residues within 4Å: Chain B: H.45 Ligand excluded by PLIP CD.15: 2 residues within 4Å: Chain B: H.47, E.76 Ligand excluded by PLIP CD.16: 2 residues within 4Å: Chain B: H.200, E.243 Ligand excluded by PLIP CD.17: 1 residues within 4Å: Chain B: H.255 Ligand excluded by PLIP CD.18: 3 residues within 4Å: Chain B: R.365, H.366, E.447 Ligand excluded by PLIP CD.19: 2 residues within 4Å: Chain B: D.393, D.395 Ligand excluded by PLIP CD.20: 1 residues within 4Å: Chain B: E.430 Ligand excluded by PLIP CD.22: 2 residues within 4Å: Chain C: H.45, K.58 Ligand excluded by PLIP CD.23: 2 residues within 4Å: Chain C: H.47, E.76 Ligand excluded by PLIP CD.24: 2 residues within 4Å: Chain C: H.200, E.243 Ligand excluded by PLIP CD.25: 3 residues within 4Å: Chain C: H.253, D.286, K.306 Ligand excluded by PLIP CD.26: 1 residues within 4Å: Chain C: H.255 Ligand excluded by PLIP CD.27: 4 residues within 4Å: Chain C: R.365, H.366, T.444, E.447 Ligand excluded by PLIP CD.28: 2 residues within 4Å: Chain C: D.393, D.395 Ligand excluded by PLIP CD.29: 1 residues within 4Å: Chain C: H.407 Ligand excluded by PLIP CD.30: 2 residues within 4Å: Chain C: E.107 Chain D: E.25 Ligand excluded by PLIP CD.31: 1 residues within 4Å: Chain C: E.340 Ligand excluded by PLIP CD.33: 1 residues within 4Å: Chain D: H.45 Ligand excluded by PLIP CD.34: 2 residues within 4Å: Chain D: H.47, E.76 Ligand excluded by PLIP CD.35: 2 residues within 4Å: Chain D: H.200, E.243 Ligand excluded by PLIP CD.36: 1 residues within 4Å: Chain D: H.255 Ligand excluded by PLIP CD.37: 3 residues within 4Å: Chain D: R.365, H.366, E.447 Ligand excluded by PLIP CD.38: 2 residues within 4Å: Chain D: D.393, D.395 Ligand excluded by PLIP CD.39: 1 residues within 4Å: Chain D: H.407 Ligand excluded by PLIP CD.40: 2 residues within 4Å: Chain C: E.25 Chain D: E.107 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hayashi, J. et al., Crystal structure of the novel amino-acid racemase isoleucine 2-epimerase from Lactobacillus buchneri. Acta Crystallogr D Struct Biol (2017)

Release Date

2017-04-19

Peptides

Isoleucine 2-epimerase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Isoleucine 2-epimerase

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