SMTL ID : 5it5.1

Thermus thermophilus PilB core ATPase region

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-hexamer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.277, C.280, C.312, C.315 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.277, A:C.280, A:C.312, A:C.315 ZN.4: 4 residues within 4Å: Chain B: C.277, C.280, C.312, C.315 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.280, B:C.315 ZN.6: 4 residues within 4Å: Chain C: C.277, C.280, C.312, C.315 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.277, C:C.280, C:C.315 ZN.9: 4 residues within 4Å: Chain D: C.277, C.280, C.312, C.315 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.277, D:C.280, D:C.312, D:C.315 ZN.12: 4 residues within 4Å: Chain E: C.277, C.280, C.312, C.315 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.277, E:C.280, E:C.312, E:C.315 ZN.14: 4 residues within 4Å: Chain F: C.277, C.280, C.312, C.315 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.277, F:C.280, F:C.312, F:C.315

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Covalent)

ATP.2: 13 residues within 4Å: Chain A: K.108, L.119, P.145, G.147, S.148, G.149, K.150, S.151, F.152, E.176, L.272, R.323, A.325 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:K.108, A:K.108, A:L.119, A:P.145, A:G.147, A:S.148, A:G.149, A:K.150, A:S.151, A:F.152, A:E.176, A:R.323 Water bridges: A:K.150 Salt bridges: A:K.150, A:K.150

5 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.3: 14 residues within 4Å: Chain B: K.108, L.119, T.146, G.147, S.148, G.149, K.150, S.151, F.152, E.176, Y.177, L.272, R.323, A.325 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:K.108, B:K.108, B:L.119, B:G.147, B:S.148, B:G.149, B:K.150, B:S.151, B:S.151, B:F.152 Water bridges: B:K.150, B:K.150, B:R.323 Salt bridges: B:K.150 AGS.5: 13 residues within 4Å: Chain C: R.77, R.90, T.146, G.147, S.148, G.149, K.150, S.151, F.152, L.272, R.323, A.325 Ligands: MG.7 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:R.90, C:L.119, C:G.147, C:S.148, C:G.149, C:G.149, C:K.150, C:K.150, C:S.151, C:F.152, C:R.323, C:R.323 Water bridges: C:A.325, C:A.325 Salt bridges: C:R.77, C:K.150 AGS.8: 15 residues within 4Å: Chain D: R.77, R.90, A.110, T.146, G.147, S.148, G.149, K.150, S.151, F.152, H.239, L.272, R.323, A.325 Ligands: MG.10 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:R.77, D:R.90, D:R.90, D:A.110, D:G.147, D:S.148, D:G.149, D:K.150, D:S.151, D:S.151, D:F.152 Salt bridges: D:R.77, D:K.150 AGS.11: 13 residues within 4Å: Chain E: K.108, L.119, T.146, G.147, S.148, G.149, K.150, S.151, F.152, E.176, L.272, R.323, A.325 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:L.119, E:G.147, E:S.148, E:G.149, E:K.150, E:K.150, E:S.151, E:S.151, E:F.152, E:R.323 Salt bridges: E:K.150 AGS.13: 14 residues within 4Å: Chain F: K.108, L.119, T.146, G.147, S.148, G.149, K.150, S.151, F.152, E.176, Y.177, L.272, R.323, A.325 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:K.108, F:L.119, F:G.147, F:S.148, F:G.149, F:K.150, F:K.150, F:S.151, F:F.152, F:Y.177, F:R.323 Water bridges: F:R.323 Salt bridges: F:K.150

2 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 3 residues within 4Å: Chain C: S.151, E.176 Ligands: AGS.5 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.151, C:E.176, H2O.6 MG.10: 3 residues within 4Å: Chain D: S.151, E.176 Ligands: AGS.8 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:S.151, H2O.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mancl, J.M. et al., Crystal Structure of a Type IV Pilus Assembly ATPase: Insights into the Molecular Mechanism of PilB from Thermus thermophilus. Structure (2016)

Release Date

2016-10-19

Peptides

ATP binding motif-containing protein PilF: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
A

C
B

D
E

E
C

F
D

ATP binding motif-containing protein PilF