SMTL ID : 5x5h.1

Crystal structure of metB from Corynebacterium glutamicum

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

homo-tetramer

Ligands

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

PLP.1: 16 residues within 4Å: Chain A: S.81, G.82, M.83, Y.107, E.150, N.154, D.179, T.181, F.182, S.201, T.203, K.204, G.214, L.333 Chain C: Y.52, R.54 8 PLIP interactions: 1 interactions with chain C, 7 interactions with chain A Salt bridges: C:R.54, A:K.204 Hydrogen bonds: A:G.82, A:M.83, A:N.154, A:S.201 Water bridges: A:E.150 pi-Stacking: A:Y.107 PLP.7: 16 residues within 4Å: Chain B: S.81, G.82, M.83, Y.107, E.150, N.154, D.179, T.181, F.182, S.201, T.203, K.204, G.214, L.333 Chain D: Y.52, R.54 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:G.82, B:M.83, B:N.154, B:T.181, B:S.201, B:T.203, B:K.204, D:Y.52 Salt bridges: B:K.204, D:R.54 pi-Stacking: B:Y.107 PLP.13: 16 residues within 4Å: Chain A: Y.52, R.54 Chain C: S.81, G.82, M.83, Y.107, E.150, N.154, D.179, T.181, F.182, S.201, T.203, K.204, G.214, L.333 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:G.82, C:M.83, C:N.154, C:T.181, C:S.201, C:T.203, C:K.204, A:Y.52 Salt bridges: C:K.204, A:R.54 pi-Stacking: C:Y.107 PLP.19: 16 residues within 4Å: Chain B: Y.52, R.54 Chain D: S.81, G.82, M.83, Y.107, E.150, N.154, D.179, T.181, F.182, S.201, T.203, K.204, G.214, L.333 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:G.82, D:M.83, D:N.154, D:S.201 Water bridges: D:E.150 Salt bridges: D:K.204, B:R.54 pi-Stacking: D:Y.107

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: D.273, T.280, V.281, L.286, N.288 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.273, A:V.281 Water bridges: A:V.281, A:N.288 GOL.3: 8 residues within 4Å: Chain A: I.15, H.16, Y.19, P.21, I.28, N.29, K.252 Chain D: E.337 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.28, A:K.252 Water bridges: A:H.16, A:H.16, A:Y.19 GOL.4: 6 residues within 4Å: Chain A: R.91, I.92, K.95, E.227, M.231 Chain C: V.117 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:I.92, A:K.95, A:E.227, A:E.227, C:T.116 GOL.8: 5 residues within 4Å: Chain B: D.273, T.280, V.281, L.286, N.288 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.273, B:V.281 Water bridges: B:V.281, B:N.288 GOL.9: 8 residues within 4Å: Chain B: I.15, H.16, Y.19, P.21, I.28, N.29, K.252 Chain C: E.337 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:I.28, B:K.252, C:E.337 Water bridges: B:H.16, B:H.16, B:Y.19 GOL.10: 6 residues within 4Å: Chain B: R.91, I.92, K.95, E.227, M.231 Chain D: V.117 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:I.92, B:K.95, B:E.227, D:T.116 GOL.14: 5 residues within 4Å: Chain C: D.273, T.280, V.281, L.286, N.288 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.273, C:V.281 Water bridges: C:V.281, C:N.288 GOL.15: 8 residues within 4Å: Chain B: E.337 Chain C: I.15, H.16, Y.19, P.21, I.28, N.29, K.252 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:I.28, C:K.252, B:E.337 Water bridges: C:H.16, C:H.16, C:Y.19 GOL.16: 6 residues within 4Å: Chain A: V.117 Chain C: R.91, I.92, K.95, E.227, M.231 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:I.92, C:K.95, C:E.227, A:T.116 GOL.20: 5 residues within 4Å: Chain D: D.273, T.280, V.281, L.286, N.288 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.273, D:V.281 Water bridges: D:V.281, D:N.288 GOL.21: 8 residues within 4Å: Chain A: E.337 Chain D: I.15, H.16, Y.19, P.21, I.28, N.29, K.252 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:I.28, D:K.252 Water bridges: D:H.16, D:H.16, D:Y.19 GOL.22: 6 residues within 4Å: Chain B: V.117 Chain D: R.91, I.92, K.95, E.227, M.231 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain D Hydrogen bonds: B:T.116, D:I.92, D:K.95, D:E.227, D:E.227

8 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain A: E.71, Q.189, P.190, L.191 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.71, A:E.71 MG.6: 6 residues within 4Å: Chain A: T.37, F.38, Q.40, E.51 Chain C: A.330, E.331 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:F.38, A:E.51 MG.11: 4 residues within 4Å: Chain B: E.71, Q.189, P.190, L.191 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.71, B:E.71 MG.12: 6 residues within 4Å: Chain B: T.37, F.38, Q.40, E.51 Chain D: A.330, E.331 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:F.38, B:E.51 MG.17: 4 residues within 4Å: Chain C: E.71, Q.189, P.190, L.191 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.71, C:E.71 MG.18: 6 residues within 4Å: Chain A: A.330, E.331 Chain C: T.37, F.38, Q.40, E.51 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:F.38, C:E.51 MG.23: 4 residues within 4Å: Chain D: E.71, Q.189, P.190, L.191 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.71, D:E.71 MG.24: 6 residues within 4Å: Chain B: A.330, E.331 Chain D: T.37, F.38, Q.40, E.51 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:F.38, D:E.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sagong, H.-Y. et al., Structural Insights into Substrate Specificity of Cystathionine gamma-Synthase from Corynebacterium glutamicum. J. Agric. Food Chem. (2017)

Release Date

2017-03-01

Peptides

Cystathionine beta-lyases/cystathionine gamma-synthases: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Cystathionine beta-lyases/cystathionine gamma-synthases