SMTL ID : 9rp1.1

Ensemble refined structure of CotB2 in complex with alendronate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

AHD.1: 14 residues within 4Å: Chain A: T.106, F.107, D.110, R.177, I.181, N.220, S.224, R.227, E.228, R.294, Y.295 Ligands: MG.2, MG.3, MG.4 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.107 Hydrogen bonds: A:R.177, A:R.177, A:I.181, A:N.220, A:N.220, A:S.224, A:R.227, A:R.227, A:R.294, A:Y.295, A:Y.295, A:Y.295 AHD.5: 13 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.6, MG.7, MG.8 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.107 Hydrogen bonds: B:R.177, B:R.177, B:I.181, B:N.220, B:S.224, B:R.227, B:R.227, B:E.228, B:E.228, B:R.294, B:Y.295 Water bridges: B:Y.295, B:Y.295

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.110 Ligands: AHD.1, MG.4 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.110, H2O.1, H2O.2 MG.3: 4 residues within 4Å: Chain A: N.220, S.224, E.228 Ligands: AHD.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.224, A:E.228 MG.4: 3 residues within 4Å: Chain A: D.110 Ligands: AHD.1, MG.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.110, H2O.1, H2O.1, H2O.2 MG.6: 3 residues within 4Å: Chain B: D.110, R.227 Ligands: AHD.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.110 MG.7: 3 residues within 4Å: Chain B: D.110, D.180 Ligands: AHD.5 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.110, H2O.4 MG.8: 5 residues within 4Å: Chain B: R.177, N.220, S.224, E.228 Ligands: AHD.5 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.224, B:E.228, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Helmer, C.P.O. et al., Ensemble refined structure of CotB2 in complex with alendronate. To Be Published

Release Date

2025-09-17

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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