SMTL ID : 7r31.1

Carbon regulatory PII-like protein SbtB from Synechocystis sp. 6803, C105A+C110A variant, in complex with ATP (co-crystal), tetragonal crystal form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

homo-trimer

Ligands

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

ATP.1: 24 residues within 4Å: Chain A: V.11, G.38, G.39, K.40, G.41, S.42, R.43, N.44, V.45, R.46, G.49, Q.50, P.51, N.59, A.88, G.89, I.90 Chain B: G.31, Y.32, T.33, E.63, I.64, L.65 Ligands: NA.2 21 PLIP interactions: 3 interactions with chain B, 18 interactions with chain A Hydrogen bonds: B:L.65, B:L.65, A:G.38, A:G.41, A:S.42, A:R.43, A:N.44, A:V.45, A:R.46, A:R.46, A:G.49, A:N.59, A:G.89 Water bridges: B:K.30, A:N.44, A:N.44, A:R.46, A:G.49, A:Q.50 Salt bridges: A:R.43, A:R.46 ATP.4: 25 residues within 4Å: Chain B: V.11, G.38, G.39, K.40, G.41, S.42, R.43, N.44, V.45, R.46, G.49, Q.50, P.51, N.59, A.88, G.89, I.90 Chain C: G.31, Y.32, T.33, E.63, I.64, L.65 Ligands: NA.5, 1PE.8 20 PLIP interactions: 16 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:G.38, B:G.39, B:G.41, B:S.42, B:R.43, B:N.44, B:V.45, B:R.46, B:R.46, B:N.59, B:G.89, C:G.31, C:L.65, C:L.65 Water bridges: B:N.44, B:G.49, B:Q.50, C:K.30 Salt bridges: B:R.43, B:R.46 ATP.6: 22 residues within 4Å: Chain A: G.31, Y.32, T.33, E.63, I.64, L.65 Chain C: V.11, G.38, G.39, K.40, G.41, S.42, R.43, N.44, V.45, R.46, S.47, N.59, A.88, G.89, I.90 Ligands: NA.7 21 PLIP interactions: 17 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:G.38, C:G.39, C:G.41, C:S.42, C:R.43, C:N.44, C:V.45, C:R.46, C:R.46, C:S.47, C:S.47, C:S.47, C:N.59, C:G.89, A:T.33, A:L.65, A:L.65 Water bridges: C:G.39, A:K.30 Salt bridges: C:R.43, C:R.46

3 x NA: SODIUM ION(Non-functional Binders)

NA.2: 3 residues within 4Å: Chain A: G.41, N.44 Ligands: ATP.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.41, A:N.44, A:N.44 Water bridges: A:Q.50 NA.5: 4 residues within 4Å: Chain B: G.41, S.42, N.44 Ligands: ATP.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.41, B:N.44, B:N.44 NA.7: 5 residues within 4Å: Chain C: G.41, S.42, N.44, S.47 Ligands: ATP.6 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.41, C:G.41, C:N.44

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

CL.3: 4 residues within 4Å: Chain A: K.61 Chain B: K.61 Chain C: M.35, K.61 Ligand excluded by PLIP

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.8: 11 residues within 4Å: Chain C: K.3, P.4, A.5, L.65, T.66, E.67, V.98, L.99, G.101, H.102 Ligands: ATP.4 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.102 Water bridges: C:G.101, C:G.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Selim, K.A. et al., Carbon signaling protein SbtB possesses atypical redox-regulated apyrase activity to facilitate regulation of bicarbonate transporter SbtA. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2023-02-15

Peptides

Membrane-associated protein slr1513: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane-associated protein slr1513