SMTL ID : 4j2h.1

Crystal structure of a putative short-chain alcohol dehydrogenase from Sinorhizobium meliloti 1021 (Target NYSGRC-011708)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

20 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 8 residues within 4Å: Chain A: Y.152, R.173, H.245, C.246 Chain B: H.245 Ligands: EDO.2, EDO.4, EDO.8 Ligand excluded by PLIP EDO.2: 7 residues within 4Å: Chain A: S.151, Y.152, L.169, R.173 Chain C: R.173 Ligands: EDO.1, EDO.16 Ligand excluded by PLIP EDO.3: 8 residues within 4Å: Chain A: S.148, L.149, I.155, Y.161, P.191, G.192, Y.193 Ligands: 1PE.7 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: R.173, G.244, H.245 Chain B: P.248, L.254 Ligands: EDO.1 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: G.141, N.183, R.185, S.236, A.240 Ligand excluded by PLIP EDO.8: 8 residues within 4Å: Chain A: H.245 Chain B: Y.152, R.173, H.245, C.246 Ligands: EDO.1, EDO.9, EDO.11 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain B: S.151, Y.152, L.169, R.173 Chain D: R.173 Ligands: EDO.8, EDO.23 Ligand excluded by PLIP EDO.10: 8 residues within 4Å: Chain B: S.148, L.149, I.155, Y.161, P.191, G.192, Y.193 Ligands: 1PE.14 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: P.248, L.254 Chain B: R.173, G.244, H.245 Ligands: EDO.8 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain B: G.141, N.183, R.185, S.236, A.240 Ligand excluded by PLIP EDO.15: 8 residues within 4Å: Chain C: Y.152, R.173, H.245, C.246 Chain D: H.245 Ligands: EDO.16, EDO.18, EDO.22 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain A: R.173 Chain C: S.151, Y.152, L.169, R.173 Ligands: EDO.2, EDO.15 Ligand excluded by PLIP EDO.17: 8 residues within 4Å: Chain C: S.148, L.149, I.155, Y.161, P.191, G.192, Y.193 Ligands: 1PE.21 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain C: R.173, G.244, H.245 Chain D: P.248, L.254 Ligands: EDO.15 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain C: G.141, N.183, R.185, S.236, A.240 Ligand excluded by PLIP EDO.22: 8 residues within 4Å: Chain C: H.245 Chain D: Y.152, R.173, H.245, C.246 Ligands: EDO.15, EDO.23, EDO.25 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain B: R.173 Chain D: S.151, Y.152, L.169, R.173 Ligands: EDO.9, EDO.22 Ligand excluded by PLIP EDO.24: 8 residues within 4Å: Chain D: S.148, L.149, I.155, Y.161, P.191, G.192, Y.193 Ligands: 1PE.28 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain C: P.248, L.254 Chain D: R.173, G.244, H.245 Ligands: EDO.22 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain D: G.141, N.183, R.185, S.236, A.240 Ligand excluded by PLIP

4 x NA: SODIUM ION(Non-functional Binders)

NA.6: 2 residues within 4Å: Chain A: Y.253, S.256 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.256, A:S.256 NA.13: 2 residues within 4Å: Chain B: Y.253, S.256 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.254, B:S.256 NA.20: 2 residues within 4Å: Chain C: Y.253, S.256 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.256, C:S.256 NA.27: 2 residues within 4Å: Chain D: Y.253, S.256 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:L.254, D:S.256

4 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.7: 13 residues within 4Å: Chain A: E.100, N.101, I.155, A.158, Y.161, Y.193, F.202, Y.203, W.208, M.212, K.215 Chain D: I.257 Ligands: EDO.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.101, A:Y.203, A:K.215 1PE.14: 13 residues within 4Å: Chain B: E.100, N.101, I.155, A.158, Y.161, Y.193, F.202, Y.203, W.208, M.212, K.215 Chain C: I.257 Ligands: EDO.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.101, B:Y.203, B:K.215 1PE.21: 13 residues within 4Å: Chain B: I.257 Chain C: E.100, N.101, I.155, A.158, Y.161, Y.193, F.202, Y.203, W.208, M.212, K.215 Ligands: EDO.17 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.100, C:N.101, C:Y.193, C:K.215 1PE.28: 13 residues within 4Å: Chain A: I.257 Chain D: E.100, N.101, I.155, A.158, Y.161, Y.193, F.202, Y.203, W.208, M.212, K.215 Ligands: EDO.24 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.100, D:N.101, D:Y.193, D:K.215

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sampathkumar, P. et al., Crystal structure of a putative short-chain alcohol dehydrogenase from Sinorhizobium meliloti 1021 (Target NYSGRC-011708). to be published

Release Date

2013-05-01

Peptides

Short chain alcohol dehydrogenase-related dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Short chain alcohol dehydrogenase-related dehydrogenase