SMTL ID : 3u0f.1

The structure of Beta-ketoacyl synthase from Brucella melitensis bound to the fragment 7-hydroxycoumarin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 5 residues within 4Å: Chain A: G.73, R.74, G.75, T.76, S.112 Ligand excluded by PLIP CL.2: 4 residues within 4Å: Chain A: D.270, M.271 Chain B: R.67, F.71 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain B: G.73, R.74, G.75, T.76, S.112 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: R.67, F.71 Chain B: D.270, M.271 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.3: 5 residues within 4Å: Chain A: N.298, P.299, E.346, S.392, N.393 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.298, A:N.393 Water bridges: A:E.346 NA.9: 5 residues within 4Å: Chain B: N.298, P.299, E.346, S.392, N.393 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.346, B:N.393

2 x 07L: 7-hydroxy-2H-chromen-2-one(Non-covalent)

07L.4: 12 residues within 4Å: Chain A: G.109, G.110, T.113, A.164, C.165, E.193, L.199, F.203, L.339 Chain B: V.136, A.139, M.140 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:A.139, B:M.140, A:A.164, A:L.199, A:F.203 Water bridges: A:G.110 07L.10: 12 residues within 4Å: Chain A: V.136, A.139, M.140 Chain B: G.109, G.110, T.113, A.164, C.165, E.193, L.199, F.203, L.339 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.164, B:L.199, B:F.203, A:A.139, A:M.140 Water bridges: B:G.110

4 x MOH: METHANOL(Non-functional Binders)

MOH.5: 5 residues within 4Å: Chain A: Y.43, H.53, L.195, D.196, W.197 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.43, A:H.53 MOH.6: 4 residues within 4Å: Chain A: M.13, T.23, D.89, Y.256 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.23 Water bridges: A:T.23, A:Y.256 MOH.11: 5 residues within 4Å: Chain B: Y.43, H.53, L.195, D.196, W.197 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.43 MOH.12: 4 residues within 4Å: Chain B: M.13, T.23, D.89, Y.256 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.23 Water bridges: B:D.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Patterson, E.I. et al., Structural characterization of beta-ketoacyl ACP synthase I bound to platencin and fragment screening molecules at two substrate binding sites. Proteins (2020)

Release Date

2011-10-12

Peptides

Beta-ketoacyl synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Beta-ketoacyl synthase