SMTL ID : 2vzy.1

Crystal structure of Rv0802c from Mycobacterium tuberculosis in an unliganded form.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 8 residues within 4Å: Chain A: Q.94, S.109, G.110, S.111, R.127, S.145, R.146, S.154 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.94, A:S.145 Water bridges: A:S.111, A:S.111 Salt bridges: A:R.127 ACT.4: 8 residues within 4Å: Chain B: Q.94, S.109, G.110, S.111, R.127, S.145, R.146, S.154 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.94, B:S.145, B:S.145 Water bridges: B:S.111, B:S.111 Salt bridges: B:R.127 ACT.7: 7 residues within 4Å: Chain C: Q.94, S.109, G.110, S.111, R.127, S.145, R.146 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.94, C:S.111 Water bridges: C:S.111 Salt bridges: C:R.127 ACT.11: 7 residues within 4Å: Chain D: Q.94, S.109, G.110, S.111, R.127, S.145, S.154 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.94, D:S.111 Water bridges: D:S.111, D:S.111 Salt bridges: D:R.127

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

SO4.2: 9 residues within 4Å: Chain A: L.113, G.119, H.120, G.121, Y.122, G.123, T.124, A.153, R.160 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.119, A:H.120, A:G.121, A:G.123, A:T.124, A:T.124, A:R.160 Water bridges: A:Y.122, A:Y.122, A:T.124, A:R.160, A:R.160, A:R.160 SO4.5: 8 residues within 4Å: Chain B: L.113, G.119, H.120, G.121, Y.122, G.123, T.124, A.153 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.119, B:G.121, B:Y.122, B:G.123, B:T.124 Water bridges: B:H.120, B:H.120, B:R.160 SO4.8: 8 residues within 4Å: Chain C: L.113, G.119, H.120, G.121, Y.122, G.123, T.124, V.157 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:G.119, C:G.121, C:Y.122, C:G.123, C:T.124 Water bridges: C:H.120, C:V.157, C:R.160 SO4.12: 8 residues within 4Å: Chain D: L.113, G.119, H.120, G.121, Y.122, G.123, T.124, A.153 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:G.119, D:H.120, D:G.121, D:Y.122, D:G.123, D:T.124, D:T.124, D:T.124

5 x ETX: 2-ETHOXYETHANOL(Non-covalent)

ETX.3: 2 residues within 4Å: Chain A: D.204, R.207 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.204, A:R.207 ETX.6: 4 residues within 4Å: Chain B: T.13, T.14, P.15, E.197 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.197 Water bridges: B:R.199 ETX.9: 8 residues within 4Å: Chain A: D.165, N.166, G.167 Chain C: D.165, N.166, G.167, L.168, L.181 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.167 ETX.10: 5 residues within 4Å: Chain C: Q.191, R.194, T.195, V.196, E.197 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.191, C:R.194 ETX.15: 4 residues within 4Å: Chain D: A.136, W.190, Q.191, R.194 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:A.136 Hydrogen bonds: D:Q.191, D:R.194 Water bridges: D:Q.191

2 x FLC: CITRATE ANION(Non-covalent)

FLC.13: 10 residues within 4Å: Chain B: R.170, E.179 Chain D: Q.141, V.142, R.184, T.186, R.187, D.188 Ligands: FLC.14, SM.16 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:Q.141, D:D.188, D:D.188 Water bridges: D:R.184, D:D.188 Salt bridges: D:R.184, B:R.170 FLC.14: 7 residues within 4Å: Chain D: R.164, R.184, T.186, D.188, D.189 Ligands: FLC.13, SM.16 4 PLIP interactions: 4 interactions with chain D Water bridges: D:R.164 Salt bridges: D:R.164, D:R.164, D:R.184

1 x SM: SAMARIUM (III) ION(Non-functional Binders)

SM.16: 2 residues within 4Å: Ligands: FLC.13, FLC.14 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vetting, M.W. et al., Rv0802C from Mycobacterium Tuberculosis: The First Structure of a Succinyltransferase with the Gnat Fold. Acta Crystallogr.,Sect.F (2008)

Release Date

2009-04-07

Peptides

RV0802C: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

RV0802C

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