SMTL ID : 3rup.1

Crystal structure of E.coli biotin carboxylase in complex with two ADP and two Ca ions

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 18 residues within 4Å: Chain A: Y.85, G.86, E.90, G.165, G.166, G.167, G.168, R.170, F.196, Q.240, K.241, N.293, R.295, Q.297, V.298, E.299, R.341, D.385 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:F.87, A:E.90, A:G.168, A:R.170, A:Q.240, A:N.293, A:R.295, A:Q.297, A:V.298, A:E.299, A:D.385 Water bridges: A:G.86, A:R.170, A:Q.240, A:R.341, A:R.341, A:R.341 Salt bridges: A:K.241, A:R.295, A:R.295, A:R.341, A:R.341 ADP.2: 21 residues within 4Å: Chain A: K.119, I.160, K.162, G.166, G.167, G.168, G.169, M.172, E.204, K.205, Y.206, L.207, H.212, Q.236, H.239, E.279, L.281, I.290, E.291, I.440 Ligands: CA.3 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.166, A:G.169, A:E.204, A:L.207, A:H.212, A:Q.236 Water bridges: A:K.119, A:K.119, A:G.168, A:G.168, A:E.279 Salt bridges: A:K.119, A:K.119, A:K.162 ADP.6: 22 residues within 4Å: Chain B: K.119, V.134, I.160, K.162, G.166, G.167, G.168, G.169, M.172, E.204, K.205, Y.206, L.207, H.212, Q.236, H.239, E.279, L.281, I.290, E.291, I.440 Ligands: CA.8 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:K.162, B:G.166, B:G.169, B:E.204, B:E.204, B:L.207, B:Q.236, B:H.239, B:E.291 Water bridges: B:K.119, B:K.119, B:G.168, B:G.168, B:H.212 Salt bridges: B:K.119, B:K.119, B:K.162 ADP.7: 17 residues within 4Å: Chain B: Y.85, G.86, F.87, E.90, G.165, G.167, G.168, F.196, Q.240, K.241, N.293, R.295, Q.297, V.298, E.299, R.341, D.385 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:F.87, B:E.90, B:E.90, B:G.168, B:Q.240, B:N.293, B:R.295, B:Q.297, B:Q.297, B:V.298 Water bridges: B:G.86, B:G.168, B:R.170, B:D.385, B:D.385, B:D.385, B:D.385 Salt bridges: B:K.241, B:R.295, B:R.295, B:R.341, B:R.341

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 3 residues within 4Å: Chain A: E.279, E.291 Ligands: ADP.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.279, A:E.291, H2O.4, H2O.7 CA.4: 3 residues within 4Å: Chain A: E.90, E.291, N.293 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.90, A:E.291, H2O.2, H2O.4, H2O.4 CA.8: 3 residues within 4Å: Chain B: E.279, E.291 Ligands: ADP.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.279, B:E.291, H2O.23, H2O.26 CA.9: 3 residues within 4Å: Chain B: E.90, E.291, N.293 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.90, B:E.291, H2O.21, H2O.23, H2O.26

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

CL.5: 4 residues within 4Å: Chain A: R.13, H.373, Y.378, P.381 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: R.13, H.373, Y.378, P.381 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain B: G.14, L.42, K.43, H.44, H.373 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chou, C.Y. et al., Structural and biochemical studies on the regulation of biotin carboxylase by substrate inhibition and dimerization. J.Biol.Chem. (2011)

Release Date

2011-05-18

Peptides

Biotin carboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Biotin carboxylase

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