SMTL ID : 2vg2.1 (1 other biounit)

Rv2361 with IPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x DPO: DIPHOSPHATE(Non-covalent)

DPO.1: 12 residues within 4Å: Chain A: M.63, D.64, G.65, N.66, G.67, R.68, R.77, H.81, R.115 Chain B: R.280, A.284 Ligands: IPE.2 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.65, A:N.66, A:G.67, A:R.68, A:R.77 Water bridges: A:M.63 Salt bridges: A:R.68, A:R.77, A:H.81, A:R.115, A:R.115, B:R.280 DPO.10: 10 residues within 4Å: Chain B: M.63, D.64, G.65, N.66, G.67, R.68, R.77, H.81, R.115 Ligands: GOL.14 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:D.64, B:G.65, B:N.66, B:G.67, B:R.68 Water bridges: B:D.64, B:S.234 Salt bridges: B:R.68, B:R.77, B:R.77, B:H.81, B:R.115, B:R.115

1 x IPE: 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

IPE.2: 15 residues within 4Å: Chain A: V.62, M.63, D.64, Y.106, S.109, N.112, R.115, R.232, R.238, S.240 Chain B: Y.249, R.280, F.281, G.282 Ligands: DPO.1 18 PLIP interactions: 6 interactions with chain B, 12 interactions with chain A Hydrogen bonds: B:Y.249, B:G.282, A:Y.106, A:Y.106, A:S.109, A:N.112, A:R.115, A:S.240 Water bridges: B:R.280, B:R.280, B:F.281 Salt bridges: B:R.280, A:R.232, A:R.232, A:R.238 Hydrophobic interactions: A:V.62, A:D.64, A:Y.106

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: T.110, W.113, P.152, R.153, N.182 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.152, A:N.182 Water bridges: A:R.153 GOL.4: 5 residues within 4Å: Chain A: W.113, K.114, R.115, S.116, P.117 3 PLIP interactions: 3 interactions with chain A Water bridges: A:W.113, A:W.113, A:R.115 GOL.5: 4 residues within 4Å: Chain A: A.52, L.55, N.57, K.101 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.57 Water bridges: A:N.57 GOL.6: 9 residues within 4Å: Chain A: T.17, W.20, P.21, V.22, K.82, M.83, E.85, A.86, R.134 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.22, A:E.85, A:E.85, A:A.86, A:R.134 Water bridges: A:T.17 GOL.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.12: 7 residues within 4Å: Chain B: A.216, L.219, R.221, P.222, I.224, Q.246 Ligands: GOL.13 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.216, B:Q.246 Water bridges: B:E.188, B:R.221 GOL.13: 6 residues within 4Å: Chain A: R.186 Chain B: E.212, A.216, D.226, W.245 Ligands: GOL.12 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.212, A:R.186 Water bridges: B:I.224, A:R.186 GOL.14: 10 residues within 4Å: Chain B: M.63, N.66, Y.106, A.107, F.108, S.109, N.112, R.115, L.123 Ligands: DPO.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.109, B:R.115 Water bridges: B:N.66

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

CL.7: 3 residues within 4Å: Chain A: R.54, T.278, R.279 Ligand excluded by PLIP

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.8: 3 residues within 4Å: Chain A: D.261, D.263, R.265 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.263, A:R.265 Water bridges: A:R.265 PO4.11: 5 residues within 4Å: Chain B: Y.106, S.109, E.111, N.112, S.240 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.109, B:N.112, B:R.115, B:S.240 Water bridges: B:Y.106 PO4.15: 2 residues within 4Å: Chain B: W.155, R.156 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.156 Salt bridges: B:R.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, W. et al., The structural basis of chain length control in Rv1086. J. Mol. Biol. (2008)

Release Date

2007-11-13

Peptides

UNDECAPRENYL PYROPHOSPHATE SYNTHETASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

UNDECAPRENYL PYROPHOSPHATE SYNTHETASE

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