SMTL ID : 4j2o.1

Crystal structure of NADP-bound WbjB from A. baumannii community strain D1279779

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-hexamer

Ligands

6 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 26 residues within 4Å: Chain A: G.30, T.32, G.33, S.34, F.35, S.55, R.56, D.57, K.60, G.78, D.79, V.80, A.99, A.100, A.101, K.103, T.118, L.141, T.143, K.157, Y.183, G.184, N.185, V.186 Chain D: D.57, K.59 27 PLIP interactions: 4 interactions with chain D, 23 interactions with chain A Hydrogen bonds: D:D.57, D:K.59, D:K.59, A:T.32, A:S.34, A:S.34, A:F.35, A:S.55, A:R.56, A:D.57, A:D.79, A:V.80, A:A.99, A:A.101, A:K.157, A:Y.183, A:Y.183 Salt bridges: D:K.59, A:R.56, A:K.60, A:K.103, A:K.103 Hydrophobic interactions: A:Y.183 Water bridges: A:G.36, A:R.56, A:K.60 pi-Cation interactions: A:R.56 NAP.2: 26 residues within 4Å: Chain B: G.30, T.32, G.33, S.34, F.35, S.55, R.56, D.57, K.60, G.78, D.79, V.80, A.99, A.100, A.101, K.103, T.118, L.141, S.142, T.143, K.157, Y.183, G.184, N.185, V.186 Chain F: K.59 25 PLIP interactions: 24 interactions with chain B, 1 interactions with chain F Hydrophobic interactions: B:Y.183 Hydrogen bonds: B:T.32, B:S.34, B:S.34, B:S.34, B:F.35, B:S.55, B:R.56, B:D.57, B:D.79, B:V.80, B:A.99, B:A.101, B:K.157, B:N.185, B:V.186 Water bridges: B:G.33, B:G.36, B:R.56 Salt bridges: B:R.56, B:K.60, B:K.103, B:K.103, F:K.59 pi-Cation interactions: B:R.56 NAP.3: 26 residues within 4Å: Chain C: G.30, T.32, G.33, S.34, F.35, S.55, R.56, D.57, K.60, G.78, D.79, V.80, A.99, A.100, A.101, K.103, T.118, L.141, S.142, T.143, K.157, Y.183, G.184, N.185, V.186 Chain E: K.59 24 PLIP interactions: 21 interactions with chain C, 3 interactions with chain E Hydrophobic interactions: C:Y.183 Hydrogen bonds: C:T.32, C:S.34, C:S.34, C:F.35, C:S.55, C:S.55, C:R.56, C:R.56, C:D.57, C:D.79, C:V.80, C:A.99, C:A.101, C:K.157, C:Y.183, E:K.59, E:K.59 Salt bridges: C:R.56, C:K.60, C:K.103, C:K.103, E:K.59 pi-Cation interactions: C:R.56 NAP.4: 25 residues within 4Å: Chain A: K.59 Chain D: G.30, T.32, G.33, S.34, F.35, S.55, R.56, D.57, K.60, G.78, D.79, V.80, A.99, A.100, A.101, K.103, T.118, L.141, S.142, T.143, K.157, Y.183, G.184, N.185 25 PLIP interactions: 23 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:T.143 Hydrogen bonds: D:T.32, D:T.32, D:S.34, D:S.34, D:F.35, D:R.56, D:D.57, D:D.79, D:V.80, D:A.99, D:A.101, D:K.157, D:N.185, A:K.59 Water bridges: D:G.33, D:G.36, D:T.118 Salt bridges: D:R.56, D:K.60, D:K.103, D:K.103, A:K.59 pi-Stacking: D:Y.183 pi-Cation interactions: D:R.56 NAP.5: 26 residues within 4Å: Chain C: K.59 Chain E: G.30, T.32, G.33, S.34, F.35, S.55, R.56, D.57, K.60, G.78, D.79, V.80, A.99, A.100, A.101, K.103, T.118, L.141, T.143, K.157, Y.183, G.184, N.185, V.186, S.189 24 PLIP interactions: 23 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:T.32, E:T.32, E:S.34, E:S.34, E:F.35, E:R.56, E:D.57, E:D.79, E:V.80, E:A.99, E:A.101, E:K.157, E:N.185, E:V.186, E:S.189, E:S.189 Water bridges: E:G.36 Salt bridges: E:R.56, E:K.60, E:K.103, E:K.103, C:K.59 pi-Stacking: E:Y.183 pi-Cation interactions: E:R.56 NAP.6: 26 residues within 4Å: Chain B: K.59 Chain F: G.30, T.32, G.33, S.34, F.35, S.55, R.56, D.57, K.60, G.78, D.79, V.80, A.99, A.100, A.101, K.103, T.118, L.141, S.142, T.143, M.153, K.157, Y.183, G.184, N.185 24 PLIP interactions: 23 interactions with chain F, 1 interactions with chain B Hydrophobic interactions: F:Y.183 Hydrogen bonds: F:T.32, F:T.32, F:S.34, F:S.34, F:F.35, F:R.56, F:D.57, F:D.79, F:V.80, F:A.99, F:A.101, F:K.157, F:G.184, F:N.185, F:V.186 Water bridges: F:R.56, F:R.81 Salt bridges: F:R.56, F:K.60, F:K.103, F:K.103, B:K.59 pi-Cation interactions: F:R.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shah, B.S. et al., Crystal structure of a UDP-GlcNAc epimerase for surface polysaccharide biosynthesis in Acinetobacter baumannii. Plos One (2018)

Release Date

2013-04-17

Peptides

UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase