SMTL ID : 6ojx.1 (1 other biounit)

PilT4 from Geobacter metallireducens bound to ATP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-hexamer

Ligands

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

EDO.1: 8 residues within 4Å: Chain A: S.37, D.38, R.50, R.118, G.154, R.298 Chain D: D.217 Ligands: ATP.6 Ligand excluded by PLIP EDO.2: 5 residues within 4Å: Chain A: D.38, R.103, V.116, R.118 Chain D: R.215 Ligand excluded by PLIP EDO.3: 6 residues within 4Å: Chain A: H.187, V.194, N.195, Q.196 Chain B: Q.109, R.110 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: P.143, R.144 Chain B: D.355, V.356, G.359, R.360 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: R.215 Chain B: D.38, R.103, V.116, R.118 Ligand excluded by PLIP EDO.8: 8 residues within 4Å: Chain A: D.217 Chain B: S.37, D.38, R.50, R.118, G.154, R.298 Ligands: ATP.10 Ligand excluded by PLIP EDO.11: 8 residues within 4Å: Chain C: S.37, D.38, R.50, R.118, G.154, R.298 Chain F: D.217 Ligands: ATP.16 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain C: D.38, R.103, V.116, R.118 Chain F: R.215 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain C: H.187, V.194, N.195, Q.196 Chain D: Q.109, R.110 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain C: P.143, R.144 Chain D: D.355, V.356, G.359, R.360 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain C: R.215 Chain D: D.38, R.103, V.116, R.118 Ligand excluded by PLIP EDO.18: 8 residues within 4Å: Chain C: D.217 Chain D: S.37, D.38, R.50, R.118, G.154, R.298 Ligands: ATP.20 Ligand excluded by PLIP EDO.21: 8 residues within 4Å: Chain B: D.217 Chain E: S.37, D.38, R.50, R.118, G.154, R.298 Ligands: ATP.26 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain B: R.215 Chain E: D.38, R.103, V.116, R.118 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain E: H.187, V.194, N.195, Q.196 Chain F: Q.109, R.110 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain E: P.143, R.144 Chain F: D.355, V.356, G.359, R.360 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain E: R.215 Chain F: D.38, R.103, V.116, R.118 Ligand excluded by PLIP EDO.28: 8 residues within 4Å: Chain E: D.217 Chain F: S.37, D.38, R.50, R.118, G.154, R.298 Ligands: ATP.30 Ligand excluded by PLIP

6 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: R.103, S.158 Ligands: ATP.6 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.158, H2O.2, H2O.2, H2O.5 MG.9: 3 residues within 4Å: Chain B: R.103, S.158 Ligands: ATP.10 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.158, H2O.13, H2O.14, H2O.17 MG.15: 3 residues within 4Å: Chain C: R.103, S.158 Ligands: ATP.16 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:S.158, H2O.26, H2O.26, H2O.29 MG.19: 3 residues within 4Å: Chain D: R.103, S.158 Ligands: ATP.20 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:S.158, H2O.37, H2O.38, H2O.41 MG.25: 3 residues within 4Å: Chain E: R.103, S.158 Ligands: ATP.26 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:S.158, H2O.49, H2O.50, H2O.53 MG.29: 3 residues within 4Å: Chain F: R.103, S.158 Ligands: ATP.30 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:S.158, H2O.61, H2O.62, H2O.65

6 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.6: 15 residues within 4Å: Chain A: S.37, R.103, R.118, L.130, T.153, G.154, S.155, G.156, K.157, S.158, T.159, L.289, R.298 Ligands: EDO.1, MG.5 28 PLIP interactions: 27 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:L.130, A:P.152, A:G.154, A:S.155, A:G.156, A:K.157, A:S.158, A:T.159, A:T.159, A:R.298 Water bridges: A:S.37, A:R.103, A:R.103, A:R.103, A:R.103, A:R.103, A:R.118, A:R.118, A:K.157, A:K.157, A:S.158, A:Q.287, D:L.214 Salt bridges: A:R.103, A:R.118, A:R.118, A:K.157, A:K.157 ATP.10: 16 residues within 4Å: Chain B: S.37, R.103, R.118, V.119, L.130, T.153, G.154, S.155, G.156, K.157, S.158, T.159, L.289, R.298 Ligands: EDO.8, MG.9 28 PLIP interactions: 27 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.130, B:P.152, B:G.154, B:S.155, B:G.156, B:K.157, B:S.158, B:T.159, B:T.159, B:R.298 Water bridges: B:R.103, B:R.103, B:R.103, B:R.103, B:R.103, B:R.118, B:R.118, B:K.157, B:K.157, B:S.158, B:Q.287, B:L.300, A:L.214 Salt bridges: B:R.103, B:R.118, B:R.118, B:K.157, B:K.157 ATP.16: 15 residues within 4Å: Chain C: S.37, R.103, R.118, L.130, T.153, G.154, S.155, G.156, K.157, S.158, T.159, L.289, R.298 Ligands: EDO.11, MG.15 28 PLIP interactions: 27 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:L.130, C:P.152, C:G.154, C:S.155, C:G.156, C:K.157, C:S.158, C:T.159, C:T.159, C:R.298 Water bridges: C:S.37, C:R.103, C:R.103, C:R.103, C:R.103, C:R.103, C:R.118, C:R.118, C:K.157, C:K.157, C:S.158, C:Q.287, F:L.214 Salt bridges: C:R.103, C:R.118, C:R.118, C:K.157, C:K.157 ATP.20: 16 residues within 4Å: Chain D: S.37, R.103, R.118, V.119, L.130, T.153, G.154, S.155, G.156, K.157, S.158, T.159, L.289, R.298 Ligands: EDO.18, MG.19 28 PLIP interactions: 27 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:L.130, D:P.152, D:G.154, D:S.155, D:G.156, D:K.157, D:S.158, D:T.159, D:T.159, D:R.298 Water bridges: D:R.103, D:R.103, D:R.103, D:R.103, D:R.103, D:R.118, D:R.118, D:K.157, D:K.157, D:S.158, D:Q.287, D:L.300, C:L.214 Salt bridges: D:R.103, D:R.118, D:R.118, D:K.157, D:K.157 ATP.26: 15 residues within 4Å: Chain E: S.37, R.103, R.118, L.130, T.153, G.154, S.155, G.156, K.157, S.158, T.159, L.289, R.298 Ligands: EDO.21, MG.25 28 PLIP interactions: 27 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:L.130, E:P.152, E:G.154, E:S.155, E:G.156, E:K.157, E:S.158, E:T.159, E:T.159, E:R.298 Water bridges: E:S.37, E:R.103, E:R.103, E:R.103, E:R.103, E:R.103, E:R.118, E:R.118, E:K.157, E:K.157, E:S.158, E:Q.287, B:L.214 Salt bridges: E:R.103, E:R.118, E:R.118, E:K.157, E:K.157 ATP.30: 16 residues within 4Å: Chain F: S.37, R.103, R.118, V.119, L.130, T.153, G.154, S.155, G.156, K.157, S.158, T.159, L.289, R.298 Ligands: EDO.28, MG.29 28 PLIP interactions: 27 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:L.130, F:P.152, F:G.154, F:S.155, F:G.156, F:K.157, F:S.158, F:T.159, F:T.159, F:R.298 Water bridges: F:R.103, F:R.103, F:R.103, F:R.103, F:R.103, F:R.118, F:R.118, F:K.157, F:K.157, F:S.158, F:Q.287, F:L.300, E:L.214 Salt bridges: F:R.103, F:R.118, F:R.118, F:K.157, F:K.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McCallum, M. et al., Multiple conformations facilitate PilT function in the type IV pilus. Nat Commun (2019)

Release Date

2019-11-20

Peptides

Twitching motility pilus retraction ATPase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Twitching motility pilus retraction ATPase

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