SMTL ID : 4hkt.1

Crystal structure of a putative myo-inositol dehydrogenase from Sinorhizobium meliloti 1021 (Target PSI-012312)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: K.246 Chain B: T.233 Chain C: T.263, G.264 Ligand excluded by PLIP EDO.2: 7 residues within 4Å: Chain A: E.260, A.262, Y.267 Chain C: E.241, A.248, V.249, A.250 Ligand excluded by PLIP EDO.3: 2 residues within 4Å: Chain A: A.202, D.205 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: R.170, D.316, V.319, R.320 Ligands: EDO.9 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: E.143, V.144, L.184, G.185, K.222 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: T.263, G.264 Chain C: K.246 Chain D: T.233 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: P.127, M.130, A.131, K.134 Chain C: V.257 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: G.204, G.207, D.208, Y.209 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: D.316, A.317, R.320, I.328 Ligands: EDO.4 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: V.319, R.320, A.323, E.324 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain B: R.239, E.252, N.253 Chain C: Y.267 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain B: R.124, R.181, F.182, D.307 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain B: E.59, E.81, R.82, R.85 Ligands: EDO.17 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain B: D.78, E.81, R.82, R.85 Ligands: EDO.16 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain B: F.125, M.130, N.286, E.289, S.290 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain B: L.98, G.166, R.170 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain B: D.153, Y.161, D.171, M.172, R.230 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain B: I.162, K.163, G.166, G.167, A.206, G.207 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain B: V.197, L.198, I.199, D.200, K.201 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain C: F.121, N.122, R.123, H.175, D.178, M.179 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain C: P.256, V.257, P.270, P.271, L.272 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain B: E.241, A.248, A.250 Chain D: E.260, Y.267 Ligand excluded by PLIP

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

NA.11: 4 residues within 4Å: Chain A: V.22, S.23, N.25, A.28 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.28, A:A.28 NA.23: 4 residues within 4Å: Chain B: V.22, S.23, N.25, A.28 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.22

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 8 residues within 4Å: Chain A: I.162, K.163, R.164, S.165, G.166, G.167, A.206, G.207 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.163, A:G.166, A:A.206 Water bridges: A:G.207, A:D.208 GOL.13: 7 residues within 4Å: Chain A: V.110, A.115, K.116, L.117, S.304, G.305, N.306 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.115, A:L.117, A:L.117, A:G.305, A:N.306 GOL.24: 7 residues within 4Å: Chain B: L.107, V.110, A.115, K.116, L.117, S.304, G.305 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.117, B:G.305 Water bridges: B:S.304, B:N.306, B:N.306 GOL.27: 10 residues within 4Å: Chain A: E.241, A.248, V.249, A.250 Chain B: R.152, Y.234, R.239 Chain C: E.260, A.262, Y.267 8 PLIP interactions: 4 interactions with chain B, 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: B:R.152, B:R.239, C:E.260, C:E.260, C:A.262, A:E.241 Water bridges: B:D.237, B:D.237 GOL.29: 9 residues within 4Å: Chain B: E.260, Y.267 Chain C: R.152, Y.234, R.239 Chain D: E.241, A.248, V.249, A.250 6 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: C:R.152, C:R.239, B:E.260, B:E.260, D:E.241 Water bridges: C:R.239

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sampathkumar, P. et al., Crystal structure of a putative myo-inositoldehydrogenase from Sinorhizobium meliloti 1021 (Target PSI-012312). to be published

Release Date

2012-12-19

Peptides

Inositol 2-dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Inositol 2-dehydrogenase