SMTL ID : 6ggi.1

Crystal structure of CotB2 in complex with 2-fluoro-3,7,18-dolabellatriene

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

9 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.110 Ligands: MG.3, PPV.6 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.110, H2O.2, H2O.3, H2O.3 MG.2: 4 residues within 4Å: Chain A: N.220, S.224, E.228 Ligands: PPV.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.224, A:E.228, H2O.1 MG.3: 3 residues within 4Å: Chain A: D.110 Ligands: MG.1, PPV.6 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.110, H2O.1, H2O.2, H2O.3, H2O.3 MG.4: 3 residues within 4Å: Chain A: E.131, Y.134, G.135 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.131, A:Y.134, H2O.2, H2O.4 MG.5: 3 residues within 4Å: Chain A: E.72, K.293, D.301 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.72, A:D.301, H2O.1, H2O.2 MG.14: 3 residues within 4Å: Chain B: D.110 Ligands: MG.15, PPV.18 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.110, H2O.8, H2O.9, H2O.9 MG.15: 3 residues within 4Å: Chain B: D.110 Ligands: MG.14, PPV.18 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.110, H2O.6, H2O.7, H2O.7, H2O.8 MG.16: 5 residues within 4Å: Chain B: R.177, N.220, S.224, E.228 Ligands: PPV.18 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.224, B:E.228, H2O.7 MG.17: 2 residues within 4Å: Chain B: D.242, S.244 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.244, H2O.7, H2O.7, H2O.8, H2O.10

2 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.6: 14 residues within 4Å: Chain A: F.107, D.110, R.177, I.181, N.220, S.224, R.227, E.228, R.294, Y.295 Ligands: MG.1, MG.2, MG.3, EXW.7 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.220, A:S.224 Water bridges: A:R.177, A:R.177, A:D.180, A:R.227, A:R.227, A:R.294 Salt bridges: A:R.177, A:R.227, A:R.294 PPV.18: 14 residues within 4Å: Chain B: F.107, D.110, R.177, I.181, N.220, S.224, R.227, E.228, R.294, Y.295 Ligands: MG.14, MG.15, MG.16, EXW.19 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:N.220, B:S.224, B:Y.295 Water bridges: B:D.110, B:D.110, B:R.177, B:R.227, B:R.227, B:R.227, B:E.228 Salt bridges: B:R.177, B:R.227, B:R.294

2 x EXW: 2-fluoro-3,7,18-dolabellatriene(Non-covalent)

EXW.7: 16 residues within 4Å: Chain A: N.103, T.106, F.107, D.110, F.149, D.180, I.181, G.182, V.183, F.185, W.186, L.216, L.281, N.285, W.288 Ligands: PPV.6 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.107, A:F.107, A:F.149, A:I.181, A:F.185, A:W.186, A:L.216, A:L.281, A:W.288 EXW.19: 17 residues within 4Å: Chain B: V.80, N.103, T.106, F.107, F.149, D.180, I.181, G.182, V.183, F.185, W.186, M.189, L.216, N.220, N.285, W.288 Ligands: PPV.18 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.80, B:F.107, B:F.149, B:I.181, B:V.183, B:F.185, B:W.186, B:L.216, B:W.288

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.8: 7 residues within 4Å: Chain A: R.175 Chain B: E.171, R.175, V.178, R.210, R.214 Ligands: MPD.20 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:E.171, B:V.178, A:R.175 Hydrogen bonds: B:R.210, A:R.175, A:R.175 Water bridges: B:R.214 MPD.20: 8 residues within 4Å: Chain A: F.174, R.175, V.178, R.210, R.214 Chain B: E.171, R.175 Ligands: MPD.8 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.178, A:R.210, B:E.171, B:R.175 Hydrogen bonds: A:R.210, A:R.214 Water bridges: A:R.214

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

CL.9: 4 residues within 4Å: Chain A: G.135, P.136, E.137, D.138 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain A: V.178, S.206, R.210 Chain B: S.206, R.210 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain B: G.135, P.136, E.137, D.138 Ligand excluded by PLIP

1 x CCN: ACETONITRILE(Non-functional Binders)

CCN.11: 4 residues within 4Å: Chain A: P.170, F.252, A.255, R.256 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.170, A:F.252 Hydrogen bonds: A:R.256

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.12: 2 residues within 4Å: Chain A: R.15, R.239 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.239 Water bridges: A:R.15, A:R.239 PEG.22: 3 residues within 4Å: Chain B: D.12, R.15, R.239 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.239 Water bridges: B:R.239

2 x K: POTASSIUM ION(Non-covalent)

K.13: 3 residues within 4Å: Chain A: A.255, D.258, D.259 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:A.255, A:D.259, H2O.2, H2O.5, H2O.6 K.23: 4 residues within 4Å: Chain B: A.255, R.256, D.258, D.259 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:A.255, H2O.6, H2O.6, H2O.10, H2O.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Driller, R. et al., Towards a comprehensive understanding of the structural dynamics of a bacterial diterpene synthase during catalysis. Nat Commun (2018)

Release Date

2018-10-10

Peptides

Cyclooctat-9-en-7-ol synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cyclooctat-9-en-7-ol synthase

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