SMTL ID : 1ny5.1

Crystal structure of sigm54 activator (AAA+ ATPase) in the inactive state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: K.173, D.238, R.357 Ligands: ADP.6 No protein-ligand interaction detected (PLIP)

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 8 residues within 4Å: Chain A: H.44, N.46, E.72, R.119, R.122, K.123 Chain B: E.224, E.228 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.46, A:R.122, B:E.224, B:E.228 Salt bridges: A:H.44, A:R.119, A:K.123 PO4.3: 7 residues within 4Å: Chain A: E.224, E.228 Chain B: H.44, N.46, E.72, R.119, K.123 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.46, A:E.228 Water bridges: B:R.119 Salt bridges: B:H.44, B:R.119, B:K.123 PO4.4: 4 residues within 4Å: Chain A: K.250, R.253, F.260, Y.261 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.261, A:Y.261 Water bridges: A:A.249, A:K.250, A:K.250 Salt bridges: A:K.250, A:R.253 PO4.5: 4 residues within 4Å: Chain A: T.340, S.342, D.376, R.377 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.342, A:S.342, A:S.342, A:R.377 Water bridges: A:S.342

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

ADP.6: 18 residues within 4Å: Chain A: E.137, E.138, Y.139, V.140, F.141, E.168, G.170, V.171, G.172, K.173, E.174, V.175, L.320, F.324, V.356, R.357, K.360 Ligands: MG.1 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:V.140, A:V.140, A:G.170, A:V.171, A:G.172, A:K.173, A:E.174, A:E.174, A:V.175, A:K.360 Water bridges: A:R.313, A:R.313, A:R.313, A:R.357, A:R.357 Salt bridges: A:K.173, A:R.357, A:R.357 pi-Stacking: A:Y.139 ADP.7: 17 residues within 4Å: Chain B: E.138, Y.139, V.140, F.141, E.168, S.169, G.170, V.171, G.172, K.173, E.174, V.175, L.320, H.323, V.356, R.357, K.360 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:V.140, B:V.140, B:G.170, B:V.171, B:G.172, B:K.173, B:E.174, B:V.175, B:K.360 Water bridges: B:Y.139, B:K.173, B:K.173, B:R.357, B:R.357, B:R.357 Salt bridges: B:K.173, B:R.357 pi-Stacking: B:Y.139

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 5 residues within 4Å: Chain A: K.331 Chain B: E.174, A.193, N.195, D.238 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.195 Water bridges: B:N.195 GOL.9: 4 residues within 4Å: Chain A: R.266, K.267 Chain B: S.41, R.69 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.267, A:K.267

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, S.Y. et al., Regulation of the transcriptional activator NtrC1: structural studies of the regulatory and AAA+ ATPase domains. Genes Dev. (2003)

Release Date

2003-11-11

Peptides

transcriptional regulator (NtrC family): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

transcriptional regulator (NtrC family)