SMTL ID : 3ouz.1 (2 other biounits)

Crystal Structure of Biotin Carboxylase-ADP complex from Campylobacter jejuni

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

13 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: E.27, M.28, D.311, E.314 Chain B: R.366, K.400 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:E.27, A:D.311, A:D.311 Water bridges: A:E.314, A:E.314, B:R.366, B:R.366, B:R.366, B:R.366 GOL.2: 3 residues within 4Å: Chain A: Y.36, K.41, L.46 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.36 Water bridges: A:L.46, A:S.52 GOL.3: 3 residues within 4Å: Chain A: I.98, K.101, H.102 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.102 GOL.4: 8 residues within 4Å: Chain A: K.124, Q.125, Q.128, V.134, I.135, P.136, G.137, S.138 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.124, A:G.137, A:S.138 Water bridges: A:G.140, A:G.140 GOL.5: 3 residues within 4Å: Chain A: W.186, S.187, S.190 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.187 GOL.9: 4 residues within 4Å: Chain A: L.116, V.126, R.129, A.269 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.129, A:R.129 Water bridges: A:I.270 GOL.12: 5 residues within 4Å: Chain A: D.42, L.44, Y.375 Chain B: K.359, I.361 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.359, A:D.42 GOL.14: 4 residues within 4Å: Chain A: R.366 Chain B: E.27, D.311, E.314 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:E.27, B:D.311 Water bridges: B:E.314, A:R.366, A:R.366, A:R.366, A:R.366 GOL.15: 4 residues within 4Å: Chain B: Y.36, K.41, L.46, S.52 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.46, B:S.52, B:S.52 Water bridges: B:Y.36 GOL.16: 3 residues within 4Å: Chain B: I.98, K.101, H.102 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.101, B:H.102 GOL.17: 3 residues within 4Å: Chain B: K.268, A.269, G.271 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.271 GOL.22: 5 residues within 4Å: Chain B: S.415, G.416, I.417, K.418 Ligands: GOL.24 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.416 GOL.24: 7 residues within 4Å: Chain B: E.345, D.346, S.347, K.418, T.419, D.422 Ligands: GOL.22 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:E.345, B:S.347, B:T.419, B:D.422, B:D.422 Water bridges: B:S.347, B:I.414, B:I.417, B:T.419

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

ADP.6: 22 residues within 4Å: Chain A: K.120, I.135, I.160, K.162, G.166, G.167, G.168, G.169, M.172, E.204, K.205, Y.206, I.207, H.212, Q.236, H.239, E.279, L.281, I.291, E.292, T.440 Ligands: MG.7 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:G.166, A:G.169, A:E.204, A:E.204, A:I.207, A:H.212, A:Q.236, A:Q.236, A:T.440 Water bridges: A:K.120, A:G.168, A:G.168, A:G.168, A:R.170, A:E.279, A:N.294 Salt bridges: A:K.120, A:K.120, A:K.162 ADP.19: 22 residues within 4Å: Chain B: K.120, I.135, I.160, K.162, G.166, G.167, G.168, G.169, M.172, E.204, K.205, Y.206, I.207, H.212, Q.236, H.239, E.279, L.281, I.291, E.292, T.440 Ligands: MG.20 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:G.167, B:G.169, B:E.204, B:I.207, B:H.212, B:Q.236, B:Q.236 Water bridges: B:K.120, B:G.168, B:G.168, B:R.170, B:Y.206, B:E.279, B:N.294, B:N.294, B:N.294 Salt bridges: B:K.120, B:K.120, B:K.162

2 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 3 residues within 4Å: Chain A: E.279, E.292 Ligands: ADP.6 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.279, A:E.292, H2O.14, H2O.14 MG.20: 3 residues within 4Å: Chain B: E.279, E.292 Ligands: ADP.19 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.279, B:E.292, H2O.32, H2O.32

5 x FMT: FORMIC ACID(Non-functional Binders)

FMT.8: 4 residues within 4Å: Chain A: D.346, S.347, K.418, T.419 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.347, A:T.419 Water bridges: A:I.417, A:T.419, A:T.419, A:D.422 FMT.11: 4 residues within 4Å: Chain A: Q.240, K.241, R.341 Ligands: SRT.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.241, A:R.341, A:R.341 Water bridges: A:Q.240 FMT.13: 3 residues within 4Å: Chain A: W.394 Chain B: G.309 Ligands: MLT.21 No protein-ligand interaction detected (PLIP) FMT.18: 3 residues within 4Å: Chain B: L.413, I.414, K.421 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.414, B:K.421 Water bridges: B:I.414 FMT.25: 4 residues within 4Å: Chain B: Q.240, K.241, R.341 Ligands: TLA.23 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:K.241, B:R.341, B:R.341 Water bridges: B:Q.240, B:Q.240, B:Q.240, B:Q.240, B:Q.240, B:K.241

1 x SRT: S,R MESO-TARTARIC ACID(Non-covalent)

SRT.10: 11 residues within 4Å: Chain A: Y.86, Q.240, K.241, E.279, N.294, R.296, Q.298, V.299, E.300, R.341 Ligands: FMT.11 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:K.241, A:N.294, A:R.296, A:Q.298, A:V.299, A:E.300, A:R.341, A:R.341 Water bridges: A:G.168, A:Q.240, A:Q.240, A:K.241 Salt bridges: A:K.241, A:K.241, A:R.296, A:R.296

1 x MLT: D-MALATE(Non-covalent)

MLT.21: 7 residues within 4Å: Chain A: M.306, N.367, W.394 Chain B: M.306, N.367, W.394 Ligands: FMT.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.367 Water bridges: B:N.367

1 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.23: 10 residues within 4Å: Chain B: Y.86, Q.240, K.241, E.279, R.296, Q.298, V.299, E.300, R.341 Ligands: FMT.25 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:Q.240, B:K.241, B:E.279, B:R.296, B:R.296, B:Q.298, B:V.299, B:R.341, B:R.341 Water bridges: B:K.241 Salt bridges: B:K.241, B:R.296

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maltseva, N. et al., Crystal Structure of Biotin Carboxylase-ADP complex from Campylobacter jejuni. TO BE PUBLISHED

Release Date

2010-10-13

Peptides

Biotin carboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Biotin carboxylase

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