SMTL ID : 5zxl.1

Structure of GldA from E.coli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.79 Å

Oligo State

homo-tetramer

Ligands

5 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.121, D.171, H.254, H.271 Ligands: GOL.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.171, A:D.171, A:H.254, A:H.271 ZN.4: 5 residues within 4Å: Chain B: D.121, D.171, H.254, H.271 Ligands: GOL.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.171, B:H.254, B:H.271 ZN.9: 5 residues within 4Å: Chain C: D.121, D.171, H.254, H.271 Ligands: GOL.10 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.171, C:D.171, C:H.254, C:H.271 ZN.16: 5 residues within 4Å: Chain D: D.121, D.171, H.254, H.271 Ligands: GOL.20 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.171, D:H.254, D:H.271 ZN.17: 3 residues within 4Å: Chain D: H.257, H.271, K.274 No protein-ligand interaction detected (PLIP)

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: D.121, A.122, L.127, D.171, F.245, L.250, H.254, H.271 Ligands: ZN.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.121, A:D.121 GOL.3: 3 residues within 4Å: Chain A: E.212, R.232 Chain B: Q.197 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.232, A:R.232, B:Q.197 Water bridges: A:E.212 GOL.5: 10 residues within 4Å: Chain B: D.121, A.122, L.127, V.129, Y.140, D.171, F.245, H.254, H.271 Ligands: ZN.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.121 GOL.6: 2 residues within 4Å: Chain B: E.212, R.232 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.232, B:R.232 GOL.7: 4 residues within 4Å: Chain A: E.231 Chain B: M.1, R.3, K.194 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:M.1, B:R.3, B:K.194, B:K.194, A:E.231 GOL.10: 8 residues within 4Å: Chain C: D.121, A.122, D.171, F.245, L.250, H.254, H.271 Ligands: ZN.9 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.121, C:H.271 GOL.11: 5 residues within 4Å: Chain C: P.228, R.232 Chain D: R.3, C.195, Q.197 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:R.232, D:C.195 GOL.12: 6 residues within 4Å: Chain A: G.341, Q.347 Chain C: M.1, R.3, K.194 Chain D: E.231 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: A:Q.347, C:M.1, D:E.231 GOL.13: 1 residues within 4Å: Chain C: R.232 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.232, C:R.232 GOL.18: 2 residues within 4Å: Chain A: N.287 Chain D: R.232 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:N.287, D:R.232, D:R.232 GOL.19: 2 residues within 4Å: Chain D: R.31, V.58 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.31 GOL.20: 7 residues within 4Å: Chain D: D.121, D.171, F.245, L.250, H.254, H.271 Ligands: ZN.16 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.121, D:H.254

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.8: 1 residues within 4Å: Chain B: Q.311 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.311 SO4.14: 1 residues within 4Å: Chain C: R.184 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.184 SO4.15: 2 residues within 4Å: Chain C: G.304, Q.311 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.311 SO4.22: 1 residues within 4Å: Chain D: Q.311 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.311 SO4.23: 3 residues within 4Å: Chain D: M.1, R.3, K.194 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:M.1, D:M.1 Salt bridges: D:R.3, D:K.194

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.21: 1 residues within 4Å: Chain D: E.60 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, J. et al., Structure of glycerol dehydrogenase (GldA) from Escherichia coli. Acta Crystallogr F Struct Biol Commun (2019)

Release Date

2019-03-20

Peptides

Glycerol dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Glycerol dehydrogenase