SMTL ID : 3tb4.1

Crystal structure of the ISC domain of VibB

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-dimer

Ligands

2 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.1: 17 residues within 4Å: Chain A: K.5, I.6, Y.39, F.40, Y.43, Q.77, R.86, L.89, W.93, G.96, L.97, Y.121, Y.147, I.150, G.151, F.176 Ligands: CA.5 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:K.5, A:I.6, A:Y.43, A:Y.43, A:F.176, A:F.176, A:F.176 Hydrogen bonds: A:Q.77, A:Q.77, A:R.86, A:R.86 Water bridges: A:Q.77, A:W.93, A:G.96, A:L.97, A:R.120, A:Y.147 BOG.6: 17 residues within 4Å: Chain B: K.5, I.6, Y.39, F.40, Y.43, Q.77, R.86, L.89, W.93, G.96, L.97, Y.121, Y.147, I.150, G.151, F.176 Ligands: CA.10 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:K.5, B:I.6, B:Y.43, B:Y.43, B:F.176, B:F.176, B:F.176 Hydrogen bonds: B:Q.77, B:Q.77, B:R.86, B:R.86 Water bridges: B:D.35, B:Q.77, B:W.93, B:G.96, B:L.97, B:R.120

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

PGE.2: 11 residues within 4Å: Chain A: H.149, L.153, D.180, F.183, S.184, Y.187 Chain B: R.186, Y.187, G.190, R.191 Ligands: PGE.7 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.186, B:R.191, B:R.191, B:R.191 PGE.7: 11 residues within 4Å: Chain A: R.186, Y.187, G.190, R.191 Chain B: H.149, L.153, D.180, F.183, S.184, Y.187 Ligands: PGE.2 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.186, A:R.191, A:R.191, A:R.191

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

EDO.3: 7 residues within 4Å: Chain A: Q.115, L.116, T.117, W.119, K.126, S.127, P.128 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.117, A:W.119, A:K.126 Water bridges: A:T.117, A:T.117 EDO.8: 7 residues within 4Å: Chain B: Q.115, L.116, T.117, W.119, K.126, S.127, P.128 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.117, B:W.119, B:K.126 Water bridges: B:T.117, B:T.117

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

PEG.4: 8 residues within 4Å: Chain A: E.38, V.41, H.42, S.46, I.51, I.55, I.104, P.106 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.42 Water bridges: A:S.46 PEG.9: 8 residues within 4Å: Chain B: E.38, V.41, H.42, S.46, I.51, I.55, I.104, P.106 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.42 Water bridges: B:S.46

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 6 residues within 4Å: Chain A: H.34, V.146, Y.147, I.150, G.151 Ligands: BOG.1 No protein-ligand interaction detected (PLIP) CA.10: 6 residues within 4Å: Chain B: H.34, V.146, Y.147, I.150, G.151 Ligands: BOG.6 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, S. et al., Structural insight into the ISC domain of VibB from Vibrio cholerae at atomic resolution: a snapshot just before the enzymatic reaction. Acta Crystallogr.,Sect.D (2012)

Release Date

2012-08-29

Peptides

Vibriobactin-specific isochorismatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Vibriobactin-specific isochorismatase