SMTL ID : 5oiu.1

Crystal structure of PilF type IV pilus assembly ATPase from Thermus thermophilus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.44 Å

Oligo State

homo-hexamer

Ligands

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

ATP.1: 13 residues within 4Å: Chain A: K.113, L.124, T.151, G.152, S.153, G.154, K.155, S.156, F.157, L.277, R.328, A.330 Ligands: MG.2 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:L.124, A:T.151, A:G.152, A:S.153, A:G.154, A:K.155, A:S.156, A:F.157, A:R.328 Water bridges: A:R.110, A:R.110, A:K.155, A:K.155, A:S.156, A:S.156, A:E.181, A:Q.275 Salt bridges: A:K.155, A:K.155 ATP.6: 13 residues within 4Å: Chain B: K.113, L.124, T.151, G.152, S.153, G.154, K.155, S.156, F.157, L.277, R.328, A.330 Ligands: MG.7 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:L.124, B:T.151, B:G.152, B:S.153, B:G.154, B:K.155, B:S.156, B:F.157, B:R.328 Water bridges: B:K.155, B:S.156, B:S.156, B:S.156, B:S.156, B:S.156 Salt bridges: B:K.155, B:K.155 ATP.11: 14 residues within 4Å: Chain C: R.82, K.113, A.115, T.151, G.152, S.153, G.154, K.155, S.156, F.157, L.277, R.328, A.330 Ligands: MG.12 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:G.152, C:S.153, C:G.154, C:K.155, C:S.156, C:F.157, C:E.181 Water bridges: C:K.155, C:K.155, C:S.156, C:S.156, C:S.156 Salt bridges: C:R.82, C:R.82, C:R.82, C:K.155, C:K.155 ATP.17: 15 residues within 4Å: Chain D: R.82, K.113, A.115, T.151, G.152, S.153, G.154, K.155, S.156, F.157, E.181, L.277, R.328, A.330 Ligands: MG.18 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:G.152, D:S.153, D:G.154, D:K.155, D:S.156, D:F.157, D:E.181 Water bridges: D:R.82, D:R.82, D:S.156, D:T.158 Salt bridges: D:R.82, D:R.82, D:K.155, D:K.155 ATP.23: 15 residues within 4Å: Chain E: K.113, L.124, P.150, T.151, G.152, S.153, G.154, K.155, S.156, F.157, Y.182, L.277, R.328, A.330 Ligands: MG.24 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:L.124, E:T.151, E:G.152, E:S.153, E:G.154, E:K.155, E:S.156, E:S.156, E:F.157, E:R.328, E:A.330 Water bridges: E:R.110 Salt bridges: E:K.155, E:K.155 ATP.27: 14 residues within 4Å: Chain F: K.113, L.124, T.151, G.152, S.153, G.154, K.155, S.156, F.157, Y.182, L.277, R.328, A.330 Ligands: MG.28 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:L.124, F:G.152, F:S.153, F:G.154, F:K.155, F:S.156, F:S.156, F:F.157, F:Y.182, F:R.328 Water bridges: F:S.156, F:S.156, F:T.158, F:E.181 Salt bridges: F:K.155, F:K.155

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: S.156, E.181 Ligands: ATP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.156, H2O.1, H2O.2 MG.7: 3 residues within 4Å: Chain B: S.156, E.181 Ligands: ATP.6 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.156, H2O.3, H2O.3, H2O.4 MG.12: 3 residues within 4Å: Chain C: S.156, E.181 Ligands: ATP.11 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:S.156, H2O.6, H2O.6, H2O.6 MG.18: 2 residues within 4Å: Chain D: S.156 Ligands: ATP.17 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:S.156, H2O.8, H2O.8, H2O.8 MG.24: 3 residues within 4Å: Chain E: S.156, E.181 Ligands: ATP.23 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:S.156, H2O.10 MG.28: 3 residues within 4Å: Chain F: S.156, E.181 Ligands: ATP.27 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:S.156, H2O.12, H2O.13, H2O.13

6 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.282, C.285, C.317, C.320 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.282, A:C.285, A:C.317, A:C.320 ZN.8: 4 residues within 4Å: Chain B: C.282, C.285, C.317, C.320 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.282, B:C.285, B:C.317, B:C.320 ZN.13: 4 residues within 4Å: Chain C: C.282, C.285, C.317, C.320 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.282, C:C.285, C:C.317, C:C.320 ZN.19: 4 residues within 4Å: Chain D: C.282, C.285, C.317, C.320 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.282, D:C.285, D:C.317, D:C.320 ZN.25: 4 residues within 4Å: Chain E: C.282, C.285, C.317, C.320 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.282, E:C.285, E:C.317, E:C.320 ZN.29: 4 residues within 4Å: Chain F: C.282, C.285, C.317, C.320 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.282, F:C.285, F:C.317, F:C.320

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

CL.4: 4 residues within 4Å: Chain A: G.152, S.153, R.276, L.277 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: T.101, V.102 Chain F: T.190, Q.191 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain B: G.152, S.153, R.276, L.277 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: T.101, V.102 Chain E: T.190, Q.191 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain B: T.190, Q.191 Chain C: T.101, V.102 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain C: Q.37, Y.49, S.50, T.51 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain C: S.153, R.276, L.277 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain A: T.190, Q.191 Chain D: P.100, T.101, V.102 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain D: Q.37, P.48, Y.49, S.50 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain D: S.153, R.276, L.277 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain E: S.153, R.276, L.277 Ligand excluded by PLIP CL.30: 5 residues within 4Å: Chain F: G.152, S.153, R.276, L.277, R.387 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Collins, R. et al., Structural cycle of the Thermus thermophilus PilF ATPase: the powering of type IVa pilus assembly. Sci Rep (2018)

Release Date

2018-08-08

Peptides

Type IV pilus assembly protein PilF: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Type IV pilus assembly protein PilF