SMTL ID : 3q2i.1

Crystal structure of the WlbA dehydrognase from Chromobactrium violaceum in complex with NADH and UDP-GlcNAcA at 1.50 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-octamer

Ligands

8 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.1: 26 residues within 4Å: Chain A: V.19, G.20, C.21, G.22, R.23, I.24, D.46, I.47, D.48, A.51, T.82, T.83, P.84, S.85, L.87, H.88, Q.91, E.105, K.106, P.107, Q.134, W.177, R.178, H.194, H.304 Ligands: HP7.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:I.24 Hydrogen bonds: A:C.21, A:C.21, A:R.23, A:I.24, A:I.47, A:T.83, A:S.85, A:E.105, A:Q.134 Water bridges: A:G.22, A:A.25, A:Q.91, A:R.178, A:R.178, A:N.190, A:N.190 Salt bridges: A:R.178, A:R.178 NAI.5: 26 residues within 4Å: Chain B: V.19, G.20, C.21, G.22, R.23, I.24, D.46, I.47, D.48, A.51, T.82, T.83, P.84, S.85, L.87, H.88, Q.91, E.105, K.106, P.107, Q.134, W.177, R.178, H.194, H.304 Ligands: HP7.6 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:I.24 Hydrogen bonds: B:C.21, B:C.21, B:R.23, B:I.24, B:I.47, B:T.83, B:S.85, B:E.105, B:Q.134 Water bridges: B:G.22, B:A.25, B:Q.91, B:R.178, B:R.178, B:N.190, B:N.190 Salt bridges: B:R.178, B:R.178 NAI.9: 26 residues within 4Å: Chain C: V.19, G.20, C.21, G.22, R.23, I.24, D.46, I.47, D.48, A.51, T.82, T.83, P.84, S.85, L.87, H.88, Q.91, E.105, K.106, P.107, Q.134, W.177, R.178, H.194, H.304 Ligands: HP7.10 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:I.24 Hydrogen bonds: C:C.21, C:C.21, C:R.23, C:I.24, C:I.47, C:T.83, C:S.85, C:E.105, C:Q.134 Water bridges: C:G.22, C:A.25, C:Q.91, C:R.178, C:R.178, C:N.190, C:N.190 Salt bridges: C:R.178, C:R.178 NAI.13: 26 residues within 4Å: Chain D: V.19, G.20, C.21, G.22, R.23, I.24, D.46, I.47, D.48, A.51, T.82, T.83, P.84, S.85, L.87, H.88, Q.91, E.105, K.106, P.107, Q.134, W.177, R.178, H.194, H.304 Ligands: HP7.14 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:I.24 Hydrogen bonds: D:C.21, D:C.21, D:R.23, D:I.24, D:I.47, D:T.83, D:S.85, D:E.105, D:Q.134 Water bridges: D:G.22, D:A.25, D:Q.91, D:R.178, D:R.178, D:N.190, D:N.190 Salt bridges: D:R.178, D:R.178 NAI.17: 26 residues within 4Å: Chain E: V.19, G.20, C.21, G.22, R.23, I.24, D.46, I.47, D.48, A.51, T.82, T.83, P.84, S.85, L.87, H.88, Q.91, E.105, K.106, P.107, Q.134, W.177, R.178, H.194, H.304 Ligands: HP7.18 19 PLIP interactions: 19 interactions with chain E Hydrophobic interactions: E:I.24 Hydrogen bonds: E:C.21, E:C.21, E:R.23, E:I.24, E:I.47, E:T.83, E:S.85, E:E.105, E:Q.134 Water bridges: E:G.22, E:A.25, E:Q.91, E:R.178, E:R.178, E:N.190, E:N.190 Salt bridges: E:R.178, E:R.178 NAI.21: 26 residues within 4Å: Chain F: V.19, G.20, C.21, G.22, R.23, I.24, D.46, I.47, D.48, A.51, T.82, T.83, P.84, S.85, L.87, H.88, Q.91, E.105, K.106, P.107, Q.134, W.177, R.178, H.194, H.304 Ligands: HP7.22 19 PLIP interactions: 19 interactions with chain F Hydrophobic interactions: F:I.24 Hydrogen bonds: F:C.21, F:C.21, F:R.23, F:I.24, F:I.47, F:T.83, F:S.85, F:E.105, F:Q.134 Water bridges: F:G.22, F:A.25, F:Q.91, F:R.178, F:R.178, F:N.190, F:N.190 Salt bridges: F:R.178, F:R.178 NAI.25: 26 residues within 4Å: Chain G: V.19, G.20, C.21, G.22, R.23, I.24, D.46, I.47, D.48, A.51, T.82, T.83, P.84, S.85, L.87, H.88, Q.91, E.105, K.106, P.107, Q.134, W.177, R.178, H.194, H.304 Ligands: HP7.26 19 PLIP interactions: 19 interactions with chain G Hydrophobic interactions: G:I.24 Hydrogen bonds: G:C.21, G:C.21, G:R.23, G:I.24, G:I.47, G:T.83, G:S.85, G:E.105, G:Q.134 Water bridges: G:G.22, G:A.25, G:Q.91, G:R.178, G:R.178, G:N.190, G:N.190 Salt bridges: G:R.178, G:R.178 NAI.29: 26 residues within 4Å: Chain H: V.19, G.20, C.21, G.22, R.23, I.24, D.46, I.47, D.48, A.51, T.82, T.83, P.84, S.85, L.87, H.88, Q.91, E.105, K.106, P.107, Q.134, W.177, R.178, H.194, H.304 Ligands: HP7.30 19 PLIP interactions: 19 interactions with chain H Hydrophobic interactions: H:I.24 Hydrogen bonds: H:C.21, H:C.21, H:R.23, H:I.24, H:I.47, H:T.83, H:S.85, H:E.105, H:Q.134 Water bridges: H:G.22, H:A.25, H:Q.91, H:R.178, H:R.178, H:N.190, H:N.190 Salt bridges: H:R.178, H:R.178

8 x HP7: (2S,3S,4R,5R,6R)-5-acetamido-6-[[[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-3,4-dihydroxy-oxane-2-carboxylic acid(Non-covalent)

HP7.2: 14 residues within 4Å: Chain A: K.106, N.135, W.165, T.166, R.167, P.168, Y.171, N.190, Q.191, H.194, Y.195, K.249, N.250 Ligands: NAI.1 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:K.106, A:K.106, A:H.194, A:N.250 Water bridges: A:N.135, A:R.167, A:R.167, A:R.178, A:N.190, A:H.194 Salt bridges: A:R.167, A:R.167, A:R.167 HP7.6: 14 residues within 4Å: Chain B: K.106, N.135, W.165, T.166, R.167, P.168, Y.171, N.190, Q.191, H.194, Y.195, K.249, N.250 Ligands: NAI.5 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:K.106, B:K.106, B:H.194, B:N.250 Water bridges: B:N.135, B:R.167, B:R.167, B:R.178, B:N.190, B:H.194 Salt bridges: B:R.167, B:R.167, B:R.167 HP7.10: 14 residues within 4Å: Chain C: K.106, N.135, W.165, T.166, R.167, P.168, Y.171, N.190, Q.191, H.194, Y.195, K.249, N.250 Ligands: NAI.9 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:K.106, C:K.106, C:H.194, C:N.250 Water bridges: C:N.135, C:R.167, C:R.167, C:R.178, C:N.190, C:H.194 Salt bridges: C:R.167, C:R.167, C:R.167 HP7.14: 14 residues within 4Å: Chain D: K.106, N.135, W.165, T.166, R.167, P.168, Y.171, N.190, Q.191, H.194, Y.195, K.249, N.250 Ligands: NAI.13 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:K.106, D:K.106, D:H.194, D:N.250 Water bridges: D:N.135, D:R.167, D:R.167, D:R.178, D:N.190, D:H.194 Salt bridges: D:R.167, D:R.167, D:R.167 HP7.18: 14 residues within 4Å: Chain E: K.106, N.135, W.165, T.166, R.167, P.168, Y.171, N.190, Q.191, H.194, Y.195, K.249, N.250 Ligands: NAI.17 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:K.106, E:K.106, E:Y.171, E:H.194, E:N.250 Water bridges: E:N.135, E:R.167, E:R.178, E:N.190, E:H.194, E:N.250 Salt bridges: E:R.167, E:R.167, E:R.167 HP7.22: 14 residues within 4Å: Chain F: K.106, N.135, W.165, T.166, R.167, P.168, Y.171, N.190, Q.191, H.194, Y.195, K.249, N.250 Ligands: NAI.21 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:K.106, F:K.106, F:Y.171, F:H.194, F:N.250 Water bridges: F:N.135, F:R.167, F:R.178, F:N.190, F:H.194, F:N.250 Salt bridges: F:R.167, F:R.167, F:R.167 HP7.26: 14 residues within 4Å: Chain G: K.106, N.135, W.165, T.166, R.167, P.168, Y.171, N.190, Q.191, H.194, Y.195, K.249, N.250 Ligands: NAI.25 14 PLIP interactions: 14 interactions with chain G Hydrogen bonds: G:K.106, G:K.106, G:Y.171, G:H.194, G:N.250 Water bridges: G:N.135, G:R.167, G:R.178, G:N.190, G:H.194, G:N.250 Salt bridges: G:R.167, G:R.167, G:R.167 HP7.30: 14 residues within 4Å: Chain H: K.106, N.135, W.165, T.166, R.167, P.168, Y.171, N.190, Q.191, H.194, Y.195, K.249, N.250 Ligands: NAI.29 14 PLIP interactions: 14 interactions with chain H Hydrogen bonds: H:K.106, H:K.106, H:Y.171, H:H.194, H:N.250 Water bridges: H:N.135, H:R.167, H:R.178, H:N.190, H:H.194, H:N.250 Salt bridges: H:R.167, H:R.167, H:R.167

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

CL.3: 3 residues within 4Å: Chain A: R.265, G.268, Q.275 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain B: R.265, G.268, Q.275 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain C: R.265, G.268, Q.275 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain D: R.265, G.268, Q.275 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain E: R.265, G.268, Q.275 Ligand excluded by PLIP CL.23: 3 residues within 4Å: Chain F: R.265, G.268, Q.275 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain G: R.265, G.268, Q.275 Ligand excluded by PLIP CL.31: 3 residues within 4Å: Chain H: R.265, G.268, Q.275 Ligand excluded by PLIP

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

NA.4: 1 residues within 4Å: Chain A: T.213 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain A Water bridges: D:R.233, D:R.233 Hydrogen bonds: A:T.213, A:T.213, A:T.213 NA.8: 1 residues within 4Å: Chain B: T.213 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:T.213, B:T.213, B:A.342 Water bridges: C:R.233, C:R.233 NA.12: 1 residues within 4Å: Chain C: T.213 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:T.213, C:T.213, C:T.213 Water bridges: A:R.233, A:R.233 NA.16: 1 residues within 4Å: Chain D: T.213 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain D Water bridges: B:R.233, B:R.233 Hydrogen bonds: D:T.213, D:T.213, D:T.213 NA.20: 1 residues within 4Å: Chain E: T.213 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain E Water bridges: H:R.233, H:R.233 Hydrogen bonds: E:T.213, E:A.342 NA.24: 1 residues within 4Å: Chain F: T.213 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain G Hydrogen bonds: F:T.213, F:A.342 Water bridges: G:R.233, G:R.233 NA.28: 1 residues within 4Å: Chain G: T.213 4 PLIP interactions: 2 interactions with chain G, 2 interactions with chain E Hydrogen bonds: G:T.213, G:A.342 Water bridges: E:R.233, E:R.233 NA.32: 1 residues within 4Å: Chain H: T.213 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain F Hydrogen bonds: H:T.213, H:A.342 Water bridges: F:R.233, F:R.233

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thoden, J.B. et al., Biochemical and Structural Characterization of WlbA from Bordetella pertussis and Chromobacterium violaceum: Enzymes Required for the Biosynthesis of 2,3-Diacetamido-2,3-dideoxy-d-mannuronic Acid. Biochemistry (2011)

Release Date

2011-01-19

Peptides

dehydrogenase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

dehydrogenase