SMTL ID : 5c7q.1

Crystal Structure of the Bdellovibrio bacteriovorus Nucleoside Diphosphate Sugar Hydrolase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: R.64, A.76, G.77, K.78 Ligands: GOL.7 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.78 Water bridges: A:Q.62, A:Q.62, A:A.76, A:K.78, A:E.92, A:E.96 Salt bridges: A:R.64, A:K.78 SO4.2: 5 residues within 4Å: Chain A: T.34, Y.35, T.36 Chain B: R.18, Q.138 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Y.19, A:T.34, A:T.36, A:T.36 Salt bridges: B:R.18 Water bridges: A:T.36 SO4.3: 4 residues within 4Å: Chain A: Y.63, R.64 Chain B: R.37, G.115 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:H.65 Water bridges: A:A.66, B:R.37 Salt bridges: A:R.64, B:R.37 SO4.12: 3 residues within 4Å: Chain A: R.37, G.115 Chain B: R.64 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain A Water bridges: B:Y.63, B:H.65, B:H.65, A:E.6, A:R.37, A:R.37, A:R.37, A:G.115 Salt bridges: B:R.64, A:R.37 SO4.13: 4 residues within 4Å: Chain A: R.18, Y.19 Chain B: Y.35, T.36 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:Y.19, B:T.34, B:T.36, B:T.36 Water bridges: A:Y.19, B:Q.26, B:Q.26, B:R.37 Salt bridges: A:R.18 SO4.14: 6 residues within 4Å: Chain B: R.64, G.77, K.78, E.96, E.140 Ligands: GOL.16 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:A.76, B:K.78 Water bridges: B:Q.62, B:Q.62, B:Q.62, B:Q.62, B:K.78, B:K.78, B:K.78, B:K.78, B:K.78, B:E.96 Salt bridges: B:R.64, B:K.78

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: L.51, L.52, P.53, R.127, D.128 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.51, A:D.128 GOL.5: 7 residues within 4Å: Chain A: Y.19, L.20, L.41, H.42, P.43, K.78 Chain B: Y.116 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.41 Water bridges: A:K.78, A:K.78, B:G.115 GOL.6: 9 residues within 4Å: Chain A: K.69, V.70, F.71, G.159, K.160, V.161, S.162 Chain B: H.111 Ligands: PG0.10 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.69, A:K.69, A:K.160, A:S.162, A:S.162 Water bridges: A:L.72 GOL.7: 8 residues within 4Å: Chain A: H.42, A.45, A.76, K.78, E.119, K.165 Chain B: Y.116 Ligands: SO4.1 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Water bridges: B:G.115 Hydrogen bonds: A:K.78, A:K.78, A:E.119, A:K.165 GOL.15: 9 residues within 4Å: Chain A: H.111 Chain B: K.69, V.70, F.71, G.159, K.160, V.161, S.162 Ligands: PG0.20 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:V.70, B:K.160, B:S.162, B:S.162 Water bridges: B:V.70, B:L.72 GOL.16: 8 residues within 4Å: Chain A: Y.116 Chain B: H.42, A.45, R.64, A.76, E.119, K.165 Ligands: SO4.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.64, B:E.119 GOL.17: 1 residues within 4Å: Chain B: H.131 No protein-ligand interaction detected (PLIP) GOL.18: 4 residues within 4Å: Chain A: V.70 Chain B: H.3, L.4, E.5 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.3, B:H.3, B:L.4, B:E.5 GOL.19: 7 residues within 4Å: Chain A: Y.116 Chain B: Y.19, L.20, L.41, H.42, P.43, K.78 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.41, A:G.115 Water bridges: B:K.78

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 6 residues within 4Å: Chain A: K.105, F.106, L.107, W.172, W.181, N.182 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.105, A:K.105 PEG.9: 4 residues within 4Å: Chain A: Q.24, Q.26, T.36 Chain B: R.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.26

2 x PG0: 2-(2-METHOXYETHOXY)ETHANOL(Non-functional Binders)

PG0.10: 4 residues within 4Å: Chain A: H.61, V.70, L.72 Ligands: GOL.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.72 PG0.20: 6 residues within 4Å: Chain B: H.61, V.70, F.71, L.72, V.145 Ligands: GOL.15 No protein-ligand interaction detected (PLIP)

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.11: 3 residues within 4Å: Chain A: P.30, D.31, G.32 No protein-ligand interaction detected (PLIP) PGE.21: 8 residues within 4Å: Chain B: K.105, L.107, L.125, R.127, W.172, F.176, W.181, N.182 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.105, B:R.127 Water bridges: B:N.182

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de la Pena, A.H. et al., Structural and Enzymatic Characterization of a Nucleoside Diphosphate Sugar Hydrolase from Bdellovibrio bacteriovorus. Plos One (2015)

Release Date

2016-01-20

Peptides

NudF protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NudF protein