SMTL ID : 5wya.1

Structure of amino acid racemase, 2.65 A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-tetramer

Ligands

4 x 7VO: (2S,3S)-3-methyl-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]pentanoic acid(Non-covalent)

7VO.1: 19 residues within 4Å: Chain A: I.24, A.54, S.114, G.115, S.116, N.119, Y.142, H.143, E.217, D.222, D.250, V.252, N.253, K.280, R.408 Chain B: Y.84, L.307, F.308, T.309 19 PLIP interactions: 15 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.24, A:Y.142, A:Y.142, A:V.252, A:N.253, B:L.307 Hydrogen bonds: A:S.114, A:G.115, A:S.116, A:D.222, A:N.253, A:K.280, B:T.309, B:T.309 Water bridges: A:S.116, A:S.116, B:T.310 Salt bridges: A:K.280, A:R.408 7VO.6: 17 residues within 4Å: Chain A: Y.84, L.307, F.308, T.309 Chain B: A.54, S.114, G.115, S.116, Y.142, H.143, G.144, E.217, D.250, V.252, N.253, K.280, R.408 21 PLIP interactions: 15 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:Y.142, B:Y.142, B:V.252, B:N.253, A:Y.84, A:L.307 Hydrogen bonds: B:G.115, B:S.116, B:N.253, B:K.280, A:Y.84, A:Y.84, A:T.309, A:T.309 Water bridges: B:S.116, B:S.116, B:E.217, B:D.222, B:D.222 Salt bridges: B:K.280, B:R.408 7VO.11: 18 residues within 4Å: Chain C: I.24, A.54, S.114, G.115, S.116, Y.142, H.143, E.217, D.222, D.250, V.252, N.253, K.280, R.408 Chain D: Y.84, L.307, F.308, T.309 16 PLIP interactions: 13 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:I.24, C:Y.142, C:Y.142, C:N.253, D:L.307 Hydrogen bonds: C:S.114, C:G.115, C:S.116, C:N.253, C:K.280, D:T.309 Water bridges: C:S.145, C:S.145, D:T.310 Salt bridges: C:K.280, C:R.408 7VO.14: 18 residues within 4Å: Chain C: Y.84, L.307, F.308, T.309 Chain D: A.54, S.114, G.115, S.116, N.119, Y.142, H.143, E.217, D.222, D.250, V.252, N.253, K.280, R.408 19 PLIP interactions: 5 interactions with chain C, 14 interactions with chain D Hydrophobic interactions: C:L.307, D:Y.142, D:Y.142, D:V.252, D:N.253 Hydrogen bonds: C:Y.84, C:Y.84, C:T.309, C:T.309, D:S.114, D:G.115, D:S.116, D:N.253, D:K.280 Water bridges: D:Y.142, D:S.145, D:E.217 Salt bridges: D:K.280, D:R.408

11 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 6 residues within 4Å: Chain A: S.178, E.187, K.227, P.229, E.230, W.363 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.187 DMS.3: 7 residues within 4Å: Chain A: Q.133, E.210 Chain C: R.127, G.131, R.132 Chain D: K.162, G.164 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:G.164 Salt bridges: A:E.210 DMS.4: 8 residues within 4Å: Chain A: K.162, G.164 Chain B: R.127, G.131, Q.133 Chain D: Q.133, E.210 Ligands: DMS.9 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:E.210 DMS.5: 4 residues within 4Å: Chain A: Y.182, E.185 Chain D: Y.182, E.185 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Salt bridges: A:E.185, D:E.185 Hydrogen bonds: D:E.185 DMS.7: 5 residues within 4Å: Chain B: S.178, E.187, K.227, P.229, W.363 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.187 DMS.8: 4 residues within 4Å: Chain B: F.202, E.203, F.239, H.243 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.203 DMS.9: 6 residues within 4Å: Chain B: Q.133 Chain C: K.162, G.164 Chain D: R.127, R.132 Ligands: DMS.4 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.210 DMS.10: 4 residues within 4Å: Chain B: Y.182 Chain C: Y.182, E.185, R.193 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Salt bridges: B:E.185, C:E.185 DMS.12: 3 residues within 4Å: Chain C: S.178, E.185, E.187 No protein-ligand interaction detected (PLIP) DMS.13: 3 residues within 4Å: Chain C: F.202, F.239, H.243 No protein-ligand interaction detected (PLIP) DMS.15: 3 residues within 4Å: Chain D: T.38, V.40, K.46 No protein-ligand interaction detected (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