SMTL ID : 3hft.1

Crystal structure of a putative polysaccharide deacetylase involved in o-antigen biosynthesis (wbms, bb0128) from bordetella bronchiseptica at 1.90 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.46, H.92, H.127 Ligands: EDO.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.46, A:D.46, A:H.92, A:H.127 ZN.9: 4 residues within 4Å: Chain B: D.46, H.92, H.127 Ligands: EDO.13 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.46, B:D.46, B:H.92, B:H.127

2 x UNL: UNKNOWN LIGAND

UNL.2: 7 residues within 4Å: Chain A: S.128, L.129, E.178, D.180 Chain B: T.133, W.166 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.178, A:E.178 UNL.10: 7 residues within 4Å: Chain A: T.133, W.166 Chain B: S.128, L.129, E.178, D.180 Ligands: EDO.13 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.178, B:E.178, A:T.133

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

EDO.3: 4 residues within 4Å: Chain A: D.46, D.180, H.208, H.211 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.180 EDO.4: 4 residues within 4Å: Chain A: G.157, I.158, V.159, Q.198 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.198 EDO.5: 10 residues within 4Å: Chain A: D.44, D.46, H.92, H.127, S.128, E.178, D.206, H.208 Ligands: ZN.1, UNL.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.128, A:H.208 EDO.6: 5 residues within 4Å: Chain A: P.153, D.155, Y.185, W.187 Chain B: R.164 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.155, A:W.187 EDO.7: 5 residues within 4Å: Chain A: D.18, N.19, K.20, F.21, N.256 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.20, A:F.21, A:F.21 EDO.11: 4 residues within 4Å: Chain B: D.46, D.180, H.208, H.211 No protein-ligand interaction detected (PLIP) EDO.12: 4 residues within 4Å: Chain B: G.157, I.158, V.159, Q.198 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.198 EDO.13: 10 residues within 4Å: Chain B: D.44, D.46, H.92, H.127, S.128, E.178, D.206, H.208 Ligands: ZN.9, UNL.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.44, B:S.128, B:H.208 EDO.14: 5 residues within 4Å: Chain A: R.164 Chain B: P.153, D.155, Y.185, W.187 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.155, B:W.187 EDO.15: 5 residues within 4Å: Chain B: D.18, N.19, K.20, F.21, N.256 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.20, B:F.21, B:F.21

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.8: 4 residues within 4Å: Chain A: V.228, D.234, R.237, W.238 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.234 MPD.16: 4 residues within 4Å: Chain B: V.228, D.234, R.237, W.238 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.234, B:D.234

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of WbmS, polysaccharide deacetylase involved in O-antigen biosynthesis (NP_886680.1) from BORDETELLA BRONCHISEPTICA at 1.90 A resolution. To be published

Release Date

2009-06-23

Peptides

WbmS, polysaccharide deacetylase involved in O-antigen biosynthesis: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

WbmS, polysaccharide deacetylase involved in O-antigen biosynthesis