SMTL ID : 1gki.1

Plasmid coupling protein TrwB in complex with ADP and Mg2+.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-hexamer

Ligands

6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 13 residues within 4Å: Chain A: A.61, T.62, G.63, T.64, G.65, K.66, S.67, V.68, L.403, I.422 Chain B: R.54, R.305 Ligands: MG.2 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:A.61, A:G.63, A:T.64, A:G.65, A:K.66, A:S.67, A:V.68, B:R.54, B:R.54, B:R.305, B:R.305 Salt bridges: A:K.66, B:R.305 ADP.3: 13 residues within 4Å: Chain B: A.61, T.62, G.63, T.64, G.65, K.66, S.67, V.68, I.422, Q.424 Chain C: R.54, R.305 Ligands: MG.4 16 PLIP interactions: 11 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:A.61, B:G.63, B:T.64, B:G.65, B:K.66, B:S.67, B:V.68, B:R.71, C:R.54, C:R.54, C:R.305 Water bridges: B:K.96, B:Q.424 Salt bridges: B:K.66, C:R.305, C:R.305 ADP.5: 14 residues within 4Å: Chain C: A.61, T.62, G.63, T.64, G.65, K.66, S.67, V.68, R.71, L.403, I.422 Chain D: R.54, R.305 Ligands: MG.6 14 PLIP interactions: 10 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:A.61, C:G.63, C:G.63, C:T.64, C:G.65, C:K.66, C:S.67, C:V.68, C:R.71, D:R.54, D:R.54 Salt bridges: C:K.66, D:R.305, D:R.305 ADP.7: 14 residues within 4Å: Chain D: A.61, T.62, G.63, T.64, G.65, K.66, S.67, V.68, L.403, I.422, Q.424 Chain E: R.54, R.305 Ligands: MG.8 15 PLIP interactions: 5 interactions with chain E, 10 interactions with chain D Hydrogen bonds: E:R.54, E:R.54, E:R.305, E:R.305, D:A.61, D:G.63, D:T.64, D:G.65, D:K.66, D:S.67, D:V.68, D:Q.424, D:Q.424 Salt bridges: E:R.305, D:K.66 ADP.11: 12 residues within 4Å: Chain E: A.61, T.62, G.63, T.64, G.65, K.66, S.67, V.68, L.403, I.422 Chain F: R.54, R.305 14 PLIP interactions: 10 interactions with chain E, 4 interactions with chain F Hydrogen bonds: E:A.61, E:G.63, E:G.63, E:T.64, E:G.65, E:K.66, E:S.67, E:S.67, E:V.68, F:R.54, F:R.54, F:R.305 Salt bridges: E:K.66 pi-Cation interactions: F:K.306 ADP.12: 13 residues within 4Å: Chain A: R.54, R.305 Chain F: A.61, G.63, T.64, G.65, K.66, S.67, V.68, R.71, L.403, I.422 Ligands: MG.13 14 PLIP interactions: 11 interactions with chain F, 3 interactions with chain A Hydrogen bonds: F:A.61, F:G.63, F:G.63, F:T.64, F:G.65, F:K.66, F:S.67, F:V.68, F:R.71, F:Q.424, A:R.54, A:R.54 Salt bridges: F:K.66, A:R.305

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: S.67 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.67 MG.4: 2 residues within 4Å: Chain B: S.67 Ligands: ADP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.67 MG.6: 2 residues within 4Å: Chain C: S.67 Ligands: ADP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.67 MG.8: 2 residues within 4Å: Chain D: S.67 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.67 MG.13: 2 residues within 4Å: Chain F: S.67 Ligands: ADP.12 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.67

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.9: 5 residues within 4Å: Chain D: E.8, S.25, G.27, K.28, R.31 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.25, D:R.31, D:R.31 Salt bridges: D:R.31 EPE.10: 2 residues within 4Å: Chain D: R.22, M.32 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.412 Salt bridges: D:R.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gomis-Ruth, F.X. et al., The Bacterial Conjugation Protein Trwb Resembles Ring Helicases and F1-ATPase. Nature (2001)

Release Date

2002-05-16

Peptides

CONJUGAL TRANSFER PROTEIN TRWB: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

E
F

F
G

CONJUGAL TRANSFER PROTEIN TRWB

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