SMTL ID : 5tsh.1

PilB from Geobacter metallireducens bound to AMP-PNP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-hexamer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.478, C.481, C.513, C.516 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.478, A:C.481, A:C.513, A:C.516 ZN.4: 4 residues within 4Å: Chain B: C.478, C.481, C.513, C.516 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.478, B:C.481, B:C.513, B:C.516 ZN.6: 4 residues within 4Å: Chain C: C.478, C.481, C.513, C.516 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.478, C:C.481, C:C.513, C:C.516 ZN.9: 4 residues within 4Å: Chain D: C.478, C.481, C.513, C.516 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.478, D:C.481, D:C.513, D:C.516 ZN.11: 4 residues within 4Å: Chain E: C.478, C.481, C.513, C.516 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.478, E:C.481, E:C.513, E:C.516 ZN.13: 4 residues within 4Å: Chain F: C.478, C.481, C.513, C.516 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.478, F:C.481, F:C.513, F:C.516

4 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.2: 15 residues within 4Å: Chain A: L.320, P.346, T.347, G.348, S.349, G.350, K.351, T.352, V.353, H.440, L.473, R.524, V.525, Y.528 Ligands: MG.3 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:L.320, A:T.347, A:T.347, A:G.348, A:S.349, A:G.350, A:K.351, A:K.351, A:K.351, A:T.352, A:V.353, A:Y.528 Water bridges: A:R.306, A:T.347, A:T.352, A:H.440, A:H.440, A:R.476 ANP.5: 13 residues within 4Å: Chain B: L.320, P.346, T.347, G.348, S.349, G.350, K.351, T.352, V.353, L.473, R.524, V.525, Y.528 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:L.320, B:G.348, B:S.349, B:G.350, B:K.351, B:K.351, B:T.352, B:T.352, B:V.353, B:R.524, B:Y.528 Water bridges: B:T.352, B:E.377 ANP.7: 16 residues within 4Å: Chain C: L.320, T.347, G.348, S.349, G.350, K.351, T.352, V.353, E.377, H.440, L.473, R.524, V.525, G.526, Y.528 Ligands: MG.8 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:L.320, C:T.347, C:G.348, C:S.349, C:G.350, C:G.350, C:K.351, C:K.351, C:T.352, C:T.352, C:V.353, C:H.440, C:G.526 Water bridges: C:S.354, C:Y.528 ANP.10: 12 residues within 4Å: Chain D: L.320, P.346, T.347, G.348, S.349, G.350, K.351, T.352, V.353, L.473, R.524, Y.528 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:L.320, D:G.348, D:S.349, D:G.350, D:K.351, D:K.351, D:T.352, D:T.352, D:T.352, D:V.353

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: T.352 Ligands: ANP.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.352, H2O.1, H2O.2, H2O.3 MG.8: 2 residues within 4Å: Chain C: T.352 Ligands: ANP.7 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.352, H2O.8, H2O.9, H2O.10

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

ADP.12: 12 residues within 4Å: Chain E: L.320, P.346, T.347, G.348, S.349, G.350, K.351, T.352, V.353, L.473, R.524, Y.528 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:P.346, E:T.347, E:G.348, E:S.349, E:G.350, E:K.351, E:T.352, E:V.353, E:Y.528, E:Y.528 Water bridges: E:R.524, E:G.526 Salt bridges: E:K.351 ADP.14: 11 residues within 4Å: Chain F: L.320, T.347, G.348, S.349, G.350, K.351, T.352, V.353, L.473, R.524, Y.528 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:L.320, F:P.346, F:G.348, F:S.349, F:S.349, F:G.350, F:K.351, F:T.352, F:T.352, F:V.353 Water bridges: F:R.306, F:R.306, F:R.524, F:G.526 Salt bridges: F:K.351

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McCallum, M. et al., The molecular mechanism of the type IVa pilus motors. Nat Commun (2017)

Release Date

2017-05-17

Peptides

Type IV pilus biogenesis ATPase PilB: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Type IV pilus biogenesis ATPase PilB

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