SMTL ID : 7ao2.1

Crystal structure of CotB2 variant W288G in complex with alendronate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

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

MPD.1: 9 residues within 4Å: Chain A: V.80, N.103, I.181, G.182, V.183, W.186, N.220, N.285 Ligands: AHD.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.186 Hydrogen bonds: A:N.103 Water bridges: A:N.220 MPD.7: 9 residues within 4Å: Chain B: V.80, N.103, I.181, G.182, V.183, W.186, N.220, N.285 Ligands: AHD.8 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.80, B:I.181, B:I.181, B:W.186, B:W.186, B:N.220 Hydrogen bonds: B:N.103 Water bridges: B:Y.295

2 x AHD: 4-AMINO-1-HYDROXYBUTANE-1,1-DIYLDIPHOSPHONATE(Non-covalent)

AHD.2: 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: MPD.1, MG.3, MG.4, MG.5 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.107 Hydrogen bonds: A:R.177, A:R.177, A:I.181, A:N.220, A:S.224, A:R.227, A:R.227, A:R.294, A:Y.295, A:Y.295, A:Y.295 Water bridges: A:D.110, A:Q.233 AHD.8: 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: MPD.7, MG.9, MG.10, MG.11 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.107, B:F.107 Hydrogen bonds: B:D.110, B:R.177, B:R.177, B:I.181, B:N.220, B:S.224, B:R.227, B:R.227, B:R.294, B:Y.295 Water bridges: B:D.180, B:D.180

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.110 Ligands: AHD.2, MG.5 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.110, H2O.2, H2O.4, H2O.4 MG.4: 4 residues within 4Å: Chain A: N.220, S.224, E.228 Ligands: AHD.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.224, A:E.228, H2O.1 MG.5: 3 residues within 4Å: Chain A: D.110 Ligands: AHD.2, MG.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.110, H2O.1, H2O.3, H2O.3, H2O.4 MG.9: 4 residues within 4Å: Chain B: D.110, R.227 Ligands: AHD.8, MG.11 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.110, H2O.9, H2O.10, H2O.11 MG.10: 4 residues within 4Å: Chain B: N.220, S.224, E.228 Ligands: AHD.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.224, B:E.228, H2O.9 MG.11: 3 residues within 4Å: Chain B: D.110 Ligands: AHD.8, MG.9 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.110, H2O.9, H2O.9, H2O.10, H2O.11

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

CL.6: 4 residues within 4Å: Chain A: K.162, Q.233, I.234, T.235 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain B: K.162, Q.233, I.234, T.235 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Raz, K. et al., The Impression of a Nonexisting Catalytic Effect: The Role of CotB2 in Guiding the Complex Biosynthesis of Cyclooctat-9-en-7-ol. J.Am.Chem.Soc. (2020)

Release Date

2020-12-02

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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