SMTL ID : 3rv4.1

Crystal structure of E.coli biotin carboxylase R16E mutant in complex with Mg-ADP and bicarbonate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 23 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: MG.2, GOL.7, MOH.8 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:Q.236, A:E.279 Salt bridges: A:K.119, A:K.119, A:K.162 ADP.11: 23 residues within 4Å: Chain B: 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: MG.12, GOL.17, MOH.18 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:G.166, B:G.169, B:E.204, B:E.204, B:L.207, B:Q.236, B:H.239 Water bridges: B:K.119, B:K.119, B:G.168, B:Q.236, B:E.279 Salt bridges: B:K.119, B:K.119, B:K.162

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: E.279, E.291 Ligands: ADP.1, MOH.8 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.279, A:E.291, H2O.4, H2O.9 MG.12: 4 residues within 4Å: Chain B: E.279, E.291 Ligands: ADP.11, MOH.18 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.279, B:E.291, H2O.18, H2O.23

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

BCT.3: 6 residues within 4Å: Chain A: K.241, R.295, Q.297, V.298, E.299, R.341 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.295, A:R.295, A:V.298, A:E.299 BCT.13: 6 residues within 4Å: Chain B: K.241, R.295, Q.297, V.298, E.299, R.341 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.295, B:R.295, B:V.298, B:E.299

2 x CS: CESIUM ION(Non-covalent)

CS.4: 3 residues within 4Å: Chain A: M.116, E.291, M.292 No protein-ligand interaction detected (PLIP) CS.14: 3 residues within 4Å: Chain B: M.116, E.291, M.292 No protein-ligand interaction detected (PLIP)

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

CL.5: 3 residues within 4Å: Chain A: N.432, G.436, T.438 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain A: H.82, G.84, R.295, I.296, Q.315 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain B: N.432, G.436, T.438 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain B: H.82, G.84, R.295, I.296, Q.315 Ligand excluded by PLIP

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

NA.6: 4 residues within 4Å: Chain A: Q.410, L.412, I.413 Chain B: L.47 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.412 NA.9: 3 residues within 4Å: Chain A: V.380, P.381, D.385 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.385 NA.16: 4 residues within 4Å: Chain A: L.47 Chain B: Q.410, L.412, I.413 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.412 NA.19: 3 residues within 4Å: Chain B: V.380, P.381, D.385 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.381

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 9 residues within 4Å: Chain A: Y.206, Q.236, R.237, R.238, H.239, I.440, H.441, E.444 Ligands: ADP.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.206, A:Q.236, A:H.239, A:H.441, A:E.444, A:E.444 GOL.17: 9 residues within 4Å: Chain B: Y.206, Q.236, R.237, R.238, H.239, I.440, H.441, E.444 Ligands: ADP.11 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.206, B:Y.206, B:Q.236, B:H.239, B:H.239, B:E.444

2 x MOH: METHANOL(Non-functional Binders)

MOH.8: 6 residues within 4Å: Chain A: G.167, G.168, E.291, N.293 Ligands: ADP.1, MG.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.293 Water bridges: A:R.295 MOH.18: 6 residues within 4Å: Chain B: G.167, G.168, E.291, N.293 Ligands: ADP.11, MG.12 4 PLIP interactions: 4 interactions with chain B Water bridges: B:E.90, B:E.291, B:E.291, B:R.295

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
A

Biotin carboxylase