SMTL ID : 9rp2.1

Ensemble refined structure of CotB2 F107A in complex with alendronate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-dimer

Ligands

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

MPD.1: 3 residues within 4Å: Chain A: P.197, E.198 Chain B: H.154 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.198 MPD.3: 9 residues within 4Å: Chain A: V.80, I.181, G.182, V.183, W.186, L.216, N.220, N.285 Ligands: AHD.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.181, A:I.181, A:W.186, A:N.220 Water bridges: A:N.103 MPD.8: 5 residues within 4Å: Chain A: E.171, V.178, R.210, R.214 Chain B: R.175 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.178 Hydrogen bonds: A:R.210, B:R.175 MPD.14: 8 residues within 4Å: Chain B: I.181, G.182, V.183, L.216, N.220, L.281, N.285 Ligands: AHD.13 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.181, B:I.181, B:L.216, B:N.220, B:L.281

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

AHD.2: 13 residues within 4Å: Chain A: D.110, R.177, I.181, N.220, S.224, R.227, E.228, R.294, Y.295 Ligands: MPD.3, MG.4, MG.5, MG.6 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.177, A:R.177, A:N.220, A:N.220, A:S.224, A:R.227, A:R.294, A:Y.295, A:Y.295 Water bridges: A:Y.295 AHD.13: 13 residues within 4Å: Chain B: D.110, R.177, I.181, N.220, S.224, R.227, E.228, R.294, Y.295 Ligands: MG.9, MG.10, MG.11, MPD.14 10 PLIP interactions: 10 interactions with chain B 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

6 x MG: MAGNESIUM ION(Non-covalent)

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.3 MG.5: 3 residues within 4Å: Chain A: D.110 Ligands: AHD.2, MG.6 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.110, H2O.5 MG.6: 3 residues within 4Å: Chain A: D.110 Ligands: AHD.2, MG.5 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.110, H2O.7, H2O.7 MG.9: 4 residues within 4Å: Chain B: D.110, R.294 Ligands: MG.10, AHD.13 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.110, H2O.5, H2O.11, H2O.13 MG.10: 4 residues within 4Å: Chain B: D.110, D.180 Ligands: MG.9, AHD.13 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.110, H2O.8, H2O.8, H2O.13 MG.11: 5 residues within 4Å: Chain B: R.177, N.220, S.224, E.228 Ligands: AHD.13 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.224, B:E.228, H2O.9

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

CL.7: 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

Helmer, C.P.O. et al., Ensemble refined structure of CotB2 F107A 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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