SMTL ID : 5d4p.1

Structure of CPII bound to ADP and bicarbonate, from Thiomonas intermedia K12

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-trimer

Ligands

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

ADP.1: 21 residues within 4Å: Chain A: I.15, G.44, K.45, G.46, S.47, H.48, G.49, Y.51, L.63, S.90, G.91, V.92, F.94 Chain C: G.35, Y.36, T.37, I.67, A.68, A.69, K.105, F.106 14 PLIP interactions: 5 interactions with chain A, 9 interactions with chain C Hydrogen bonds: A:S.47, A:H.48, A:G.49, A:Y.51, A:G.91, C:Y.36, C:T.37, C:A.69, C:A.69 Water bridges: C:K.34, C:K.105, C:K.105 Salt bridges: C:K.105, C:K.105 ADP.3: 21 residues within 4Å: Chain A: G.35, Y.36, T.37, I.67, A.68, A.69, K.105, F.106 Chain B: I.15, G.44, K.45, G.46, S.47, H.48, G.49, Y.51, L.63, S.90, G.91, V.92, F.94 12 PLIP interactions: 7 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:Y.36, A:A.69, A:A.69, B:S.47, B:H.48, B:G.49, B:S.90, B:G.91 Water bridges: A:K.34, A:R.102 Salt bridges: A:K.105, A:K.105 ADP.7: 22 residues within 4Å: Chain B: K.34, G.35, Y.36, T.37, I.67, A.68, A.69, K.105, F.106 Chain C: I.15, G.44, K.45, G.46, S.47, H.48, G.49, Y.51, L.63, S.90, G.91, V.92, F.94 17 PLIP interactions: 7 interactions with chain B, 10 interactions with chain C Hydrogen bonds: B:Y.36, B:A.69, B:A.69, C:K.45, C:S.47, C:S.47, C:H.48, C:G.49, C:G.91 Water bridges: B:K.34, B:R.102, C:G.46, C:G.46, C:S.90, C:S.90 Salt bridges: B:K.105, B:K.105

7 x BCT: BICARBONATE ION(Non-functional Binders)

BCT.2: 6 residues within 4Å: Chain A: V.100, G.101, R.102, F.106 Chain B: V.92, V.93 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.101, B:V.93 BCT.4: 7 residues within 4Å: Chain B: V.100, G.101, R.102, F.106 Chain C: V.92, V.93 Ligands: BCT.6 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:V.93, B:G.101, B:R.102, B:R.102, B:R.102 BCT.5: 3 residues within 4Å: Chain A: R.102 Chain B: Q.83, F.86 No protein-ligand interaction detected (PLIP) BCT.6: 4 residues within 4Å: Chain B: R.102 Chain C: L.79, Q.83 Ligands: BCT.4 No protein-ligand interaction detected (PLIP) BCT.8: 7 residues within 4Å: Chain A: V.92, V.93 Chain C: V.100, G.101, R.102, F.106 Ligands: BCT.9 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.101, C:R.102, C:R.102 BCT.9: 4 residues within 4Å: Chain A: Q.83 Chain C: G.101, R.102 Ligands: BCT.8 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.102 BCT.10: 2 residues within 4Å: Chain C: F.23, H.89 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wheatley, N.M. et al., A PII-Like Protein Regulated by Bicarbonate: Structural and Biochemical Studies of the Carboxysome-Associated CPII Protein. J.Mol.Biol. (2016)

Release Date

2016-09-28

Peptides

Putative Nitrogen regulatory protein P-II GlnB: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Putative Nitrogen regulatory protein P-II GlnB

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