SMTL ID : 5krr.1

1-deoxy-D-xylulose 5-phosphate reductoisomerase from Vibrio vulnificus in complex with Mn(2+)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 3 residues within 4Å: Chain A: C.174, D.175, Q.179 Ligand excluded by PLIP

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

EDO.2: 7 residues within 4Å: Chain A: L.125, K.128, P.151, V.152, D.153, H.156, E.237 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.128, A:K.128, A:V.152, A:D.153, A:H.156 EDO.3: 6 residues within 4Å: Chain A: Q.161, L.163, P.164 Chain B: Q.161, C.162, L.163 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:L.163, A:L.163 Water bridges: B:Q.168, A:Q.168 EDO.5: 8 residues within 4Å: Chain B: L.125, N.127, K.128, P.151, V.152, D.153, H.156, E.237 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.128, B:V.152, B:D.153 EDO.6: 6 residues within 4Å: Chain B: Q.136, I.139, E.143, G.172, R.173, W.240 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.136, B:Q.136 EDO.7: 6 residues within 4Å: Chain B: E.155, G.188, S.189, S.225, K.231, S.257 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.189, B:S.257 Water bridges: B:E.155, B:T.187, B:S.189, B:G.190, B:S.225, B:K.231, B:K.231, B:K.231

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.4: 4 residues within 4Å: Chain A: E.155, N.230, K.231, E.234 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.155, A:E.234, H2O.1, H2O.3, H2O.4 MN.8: 3 residues within 4Å: Chain B: D.153, E.155, E.234 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.153, B:E.155, B:E.234, H2O.5, H2O.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ussin, N.K. et al., Structural characterization of 1-deoxy-D-xylulose 5-phosphate Reductoisomerase from Vibrio vulnificus. Biochim Biophys Acta Proteins Proteom (2018)

Release Date

2017-07-12

Peptides

1-deoxy-D-xylulose 5-phosphate reductoisomerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

1-deoxy-D-xylulose 5-phosphate reductoisomerase

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