SMTL ID : 3m0e.1

Crystal structure of the ATP-bound state of Walker B mutant of NtrC1 ATPase domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.63 Å

Oligo State

homo-heptamer

Ligands

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

ATP.1: 19 residues within 4Å: Chain A: Y.18, V.19, E.47, S.48, G.49, V.50, G.51, K.52, E.53, V.54, N.159, L.199, F.203, V.235, R.236, K.239 Chain B: D.174, R.178 Ligands: MG.2 19 PLIP interactions: 16 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:V.19, A:V.19, A:G.49, A:V.50, A:G.51, A:K.52, A:E.53, A:V.54, A:N.159 Water bridges: A:R.192, B:R.178, B:R.178 Salt bridges: A:K.52, A:K.52, A:R.236, A:R.236, A:R.236, B:R.178 pi-Stacking: A:Y.18 ATP.3: 18 residues within 4Å: Chain B: Y.18, V.19, E.47, S.48, G.49, V.50, G.51, K.52, E.53, V.54, N.159, L.199, V.235, R.236, K.239 Chain C: D.174, R.178 Ligands: MG.4 24 PLIP interactions: 6 interactions with chain C, 18 interactions with chain B Water bridges: C:D.174, C:R.178, C:R.178, C:R.178, C:R.178, B:R.192, B:R.236 Salt bridges: C:R.178, B:K.52, B:K.52, B:R.236, B:R.236, B:R.236 Hydrogen bonds: B:V.19, B:V.19, B:G.49, B:V.50, B:G.51, B:G.51, B:K.52, B:E.53, B:V.54, B:N.159 pi-Stacking: B:Y.18 ATP.5: 18 residues within 4Å: Chain C: Y.18, V.19, E.47, S.48, G.49, V.50, G.51, K.52, E.53, V.54, N.159, L.199, V.235, R.236, K.239 Chain D: D.174, R.178 Ligands: MG.6 20 PLIP interactions: 19 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:V.19, C:V.19, C:E.47, C:G.49, C:V.50, C:G.51, C:K.52, C:E.53, C:V.54, C:N.159 Water bridges: C:E.53, C:E.53, C:R.236 Salt bridges: C:K.52, C:K.52, C:R.236, C:R.236, C:R.236, D:R.178 pi-Stacking: C:Y.18 ATP.7: 19 residues within 4Å: Chain D: Y.18, V.19, E.47, S.48, G.49, V.50, G.51, K.52, E.53, V.54, N.159, L.199, F.203, V.235, R.236, K.239 Chain E: D.174, R.178 Ligands: MG.8 21 PLIP interactions: 19 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:V.19, D:V.19, D:G.49, D:V.50, D:G.51, D:K.52, D:E.53, D:V.54, D:N.159 Water bridges: D:E.53, D:E.53, D:N.159, D:R.236, E:D.174 Salt bridges: D:K.52, D:K.52, D:R.236, D:R.236, D:R.236, E:R.178 pi-Stacking: D:Y.18 ATP.9: 19 residues within 4Å: Chain E: Y.18, V.19, E.47, S.48, G.49, V.50, G.51, K.52, E.53, V.54, N.159, L.199, F.203, V.235, R.236, K.239 Chain F: D.174, R.178 Ligands: MG.10 20 PLIP interactions: 18 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:V.19, E:V.19, E:G.49, E:V.50, E:G.51, E:K.52, E:E.53, E:V.54, E:N.159 Water bridges: E:Y.18, E:E.53, E:R.192, F:R.178 Salt bridges: E:K.52, E:K.52, E:R.236, E:R.236, E:R.236, F:R.178 pi-Stacking: E:Y.18 ATP.11: 18 residues within 4Å: Chain F: Y.18, V.19, E.47, S.48, G.49, V.50, G.51, K.52, E.53, V.54, N.159, L.199, V.235, R.236, K.239 Chain G: D.174, R.178 Ligands: MG.12 20 PLIP interactions: 18 interactions with chain F, 2 interactions with chain G Hydrogen bonds: F:V.19, F:V.19, F:G.49, F:V.50, F:G.51, F:G.51, F:K.52, F:E.53, F:V.54, F:N.159 Water bridges: F:R.192, F:R.236, G:R.178 Salt bridges: F:K.52, F:K.52, F:R.236, F:R.236, F:R.236, G:R.178 pi-Stacking: F:Y.18 ATP.13: 19 residues within 4Å: Chain A: D.174, R.178 Chain G: Y.18, V.19, E.47, S.48, G.49, V.50, G.51, K.52, E.53, V.54, N.159, L.199, F.203, V.235, R.236, K.239 Ligands: MG.14 22 PLIP interactions: 19 interactions with chain G, 3 interactions with chain A Hydrogen bonds: G:V.19, G:V.19, G:G.49, G:V.50, G:G.51, G:K.52, G:E.53, G:V.54, G:N.159 Water bridges: G:E.53, G:R.192, G:R.236, G:R.236, A:D.174, A:R.178 Salt bridges: G:K.52, G:K.52, G:R.236, G:R.236, G:R.236, A:R.178 pi-Stacking: G:Y.18

7 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: E.53, D.117 Chain B: R.178 Ligands: ATP.1 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain B: E.53, D.117 Chain C: R.178 Ligands: ATP.3 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain C: E.53, D.117 Ligands: ATP.5 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain D: E.53, D.117 Ligands: ATP.7 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain E: E.53, D.117 Chain F: R.178 Ligands: ATP.9 No protein-ligand interaction detected (PLIP) MG.12: 4 residues within 4Å: Chain F: E.53, D.117 Chain G: R.178 Ligands: ATP.11 No protein-ligand interaction detected (PLIP) MG.14: 4 residues within 4Å: Chain A: R.178 Chain G: E.53, D.117 Ligands: ATP.13 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, B. et al., Engagement of Arginine Finger to ATP Triggers Large Conformational Changes in NtrC1 AAA+ ATPase for Remodeling Bacterial RNA Polymerase. Structure (2010)

Release Date

2010-11-03

Peptides

Transcriptional regulator (NtrC family): ABCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

Transcriptional regulator (NtrC family)