SMTL ID : 8qws.1

Crystal structure of CotB2 variant V80L in complex with alendronate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 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: 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, MPD.8 16 PLIP interactions: 16 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:E.228, A:E.228, A:R.294, A:Y.295, A:Y.295 Water bridges: A:N.220, A:Q.233, A:Y.295 AHD.17: 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.18, MG.19, MG.20, MPD.26 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.107 Hydrogen bonds: B:R.177, B:R.177, B:I.181, B:S.224, B:R.227, B:R.227, B:R.294 Water bridges: B:D.180, B:D.180, B:Q.233, B:Y.295, B:Y.295

7 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.110 Ligands: AHD.1, MG.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.110, H2O.2, H2O.3, H2O.3 MG.3: 5 residues within 4Å: Chain A: R.177, N.220, S.224, E.228 Ligands: AHD.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.224, A:E.228, H2O.1 MG.4: 3 residues within 4Å: Chain A: D.110 Ligands: AHD.1, MG.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.110, H2O.1, H2O.1, H2O.1, H2O.2 MG.18: 3 residues within 4Å: Chain B: D.110 Ligands: AHD.17, MG.20 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.110, H2O.7, H2O.8, H2O.9 MG.19: 5 residues within 4Å: Chain B: R.177, N.220, S.224, E.228 Ligands: AHD.17 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.224, B:E.228, H2O.7 MG.20: 3 residues within 4Å: Chain B: D.110 Ligands: AHD.17, MG.18 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.110, H2O.7, H2O.7, H2O.7, H2O.8 MG.21: 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

11 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 7 residues within 4Å: Chain A: A.145, A.148, F.149, T.179, D.184, F.185 Chain B: T.205 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:T.205, A:A.145, A:F.185 Water bridges: A:D.184, A:S.206 EDO.6: 6 residues within 4Å: Chain A: R.175 Chain B: F.174, V.178, R.210, R.214 Ligands: ACT.25 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Water bridges: B:R.175, B:R.210, B:T.213 Hydrogen bonds: A:R.175 EDO.7: 4 residues within 4Å: Chain A: P.20, Y.21, S.244, E.246 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.244 EDO.9: 2 residues within 4Å: Chain A: T.68, S.70 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.68 EDO.11: 2 residues within 4Å: Chain A: D.111, M.112 No protein-ligand interaction detected (PLIP) EDO.12: 3 residues within 4Å: Chain A: R.147, T.151 Chain B: E.201 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.147, A:T.151, A:T.151 Water bridges: B:E.201 EDO.16: 4 residues within 4Å: Chain A: T.200, E.201, K.204 Chain B: R.147 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.201, A:K.204 Water bridges: A:E.201 EDO.23: 1 residues within 4Å: Chain B: P.197 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.197 EDO.24: 2 residues within 4Å: Chain A: P.197 Chain B: T.151 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.197 EDO.27: 7 residues within 4Å: Chain A: T.205 Chain B: A.145, A.148, F.149, T.179, D.184, F.185 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.145, B:D.184, A:T.205 Water bridges: B:F.185, B:F.185, B:S.206 EDO.29: 4 residues within 4Å: Chain B: P.170, F.252, A.255, R.256 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.256, B:R.256

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

MPD.8: 9 residues within 4Å: Chain A: L.80, I.181, G.182, V.183, W.186, N.220, N.285, W.288 Ligands: AHD.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.181, A:W.186, A:N.220 Water bridges: A:N.220, A:N.285 MPD.26: 8 residues within 4Å: Chain B: L.80, N.103, I.181, G.182, W.186, M.189, L.216 Ligands: AHD.17 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.80, B:I.181, B:L.216 Water bridges: B:N.285 MPD.31: 5 residues within 4Å: Chain B: D.12, R.15, Y.225, V.229, R.239 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:R.15 MPD.32: 7 residues within 4Å: Chain B: D.57, A.60, A.61, Q.125, K.128, I.129, K.132 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:D.57, B:I.129 Hydrogen bonds: B:D.57

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.10: 6 residues within 4Å: Chain A: R.157, D.158, K.162, G.232, Q.233, I.234 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.234 Hydrogen bonds: A:D.158, A:I.234 Salt bridges: A:K.162 ACT.13: 3 residues within 4Å: Chain A: P.20, Y.21, E.246 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.20 ACT.14: 3 residues within 4Å: Chain A: E.45, E.50, M.93 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.45 ACT.25: 5 residues within 4Å: Chain A: R.175, V.178, R.210 Chain B: R.175 Ligands: EDO.6 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:R.175, A:R.214 Salt bridges: B:R.175 Hydrophobic interactions: A:V.178 ACT.28: 6 residues within 4Å: Chain B: R.157, D.158, K.162, G.232, Q.233, I.234 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.234 Hydrogen bonds: B:D.158, B:D.158, B:I.234, B:T.235 Salt bridges: B:K.162

2 x PG0: 2-(2-METHOXYETHOXY)ETHANOL(Non-functional Binders)

PG0.15: 4 residues within 4Å: Chain A: H.117, D.118, F.119, G.120 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.119, A:G.120 PG0.30: 4 residues within 4Å: Chain B: H.117, D.118, F.119, G.120 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.119, B:G.120

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

CL.22: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Himpich, S. et al., How Can the Diterpene Synthase CotB2V80L Alter the Product Profile?. Chemcatchem (2024)

Release Date

2024-04-24

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

Related Entries With Identical Sequence