SMTL ID : 8qm1.1

wild type Pa.FabF in complex cerulenin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-dimer

Ligands

18 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.1: 10 residues within 4Å: Chain A: R.4, R.5, V.7, A.176, R.177, A.180, L.259, V.260, G.261, D.291 Ligand excluded by PLIP DMS.3: 5 residues within 4Å: Chain A: R.70, L.72, D.73, Q.77, N.115 Ligand excluded by PLIP DMS.4: 4 residues within 4Å: Chain A: H.41, V.55, L.74, M.194 Ligand excluded by PLIP DMS.5: 4 residues within 4Å: Chain A: R.213, R.219, R.222, D.227 Ligand excluded by PLIP DMS.6: 8 residues within 4Å: Chain A: A.46, Y.47, S.48, G.202, G.205, A.206 Chain B: P.128, R.129 Ligand excluded by PLIP DMS.7: 3 residues within 4Å: Chain A: G.35, A.37, K.56 Ligand excluded by PLIP DMS.8: 4 residues within 4Å: Chain A: I.314, K.321, E.375, G.376 Ligand excluded by PLIP DMS.9: 3 residues within 4Å: Chain A: K.286, R.290, P.296 Ligand excluded by PLIP DMS.10: 3 residues within 4Å: Chain A: G.57, F.58, N.59 Ligand excluded by PLIP DMS.13: 8 residues within 4Å: Chain B: R.4, A.176, R.177, A.180, V.260, G.261, F.262, D.291 Ligand excluded by PLIP DMS.15: 5 residues within 4Å: Chain B: A.69, R.70, L.72, Q.77, N.115 Ligand excluded by PLIP DMS.16: 3 residues within 4Å: Chain B: H.41, L.74, M.194 Ligand excluded by PLIP DMS.17: 3 residues within 4Å: Chain B: R.213, R.222, D.227 Ligand excluded by PLIP DMS.18: 6 residues within 4Å: Chain A: R.129 Chain B: A.46, Y.47, S.48, G.205, A.206 Ligand excluded by PLIP DMS.19: 5 residues within 4Å: Chain B: S.34, G.35, I.36, A.37, K.56 Ligand excluded by PLIP DMS.20: 4 residues within 4Å: Chain B: I.314, I.317, E.375, G.376 Ligand excluded by PLIP DMS.21: 5 residues within 4Å: Chain B: K.286, L.289, R.290, L.294, P.296 Ligand excluded by PLIP DMS.22: 3 residues within 4Å: Chain B: G.57, F.58, N.59 Ligand excluded by PLIP

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 3 residues within 4Å: Chain A: L.92, E.93, V.94 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.94 FMT.14: 3 residues within 4Å: Chain B: L.92, E.93, V.94 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.94

2 x CER: (2S, 3R)-3-HYDROXY-4-OXO-7,10-TRANS,TRANS-DODECADIENAMIDE(Covalent)

CER.11: 18 residues within 4Å: Chain A: G.109, I.110, L.113, A.164, C.165, E.193, A.195, G.200, F.204, H.305, T.307, H.342, L.344, F.399, G.400, F.401 Chain B: V.136, I.140 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.110, A:I.110, A:I.110, A:L.113, A:A.164, A:A.195, A:F.204, A:F.204, A:F.401, B:V.136, B:I.140 Hydrogen bonds: A:C.165, A:H.342, A:F.401 CER.23: 16 residues within 4Å: Chain A: V.136, I.140 Chain B: G.109, I.110, L.113, A.164, C.165, E.193, F.204, F.231, H.305, T.307, H.342, F.399, G.400, F.401 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.110, B:I.110, B:L.113, B:A.164, B:F.204, B:F.204, A:V.136, A:I.140 Hydrogen bonds: B:C.165, B:F.401

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.12: 4 residues within 4Å: Chain A: R.297, Q.298, D.300, D.392 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.300

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Georgiou, C. et al., New starting points for antibiotics targeting P. aeruginosa FabF discovered by crystallographic fragment screening followed by hit expansion. Chemrxiv (2023)

Release Date

2024-01-10

Peptides

3-oxoacyl-[acyl-carrier-protein] synthase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3-oxoacyl-[acyl-carrier-protein] synthase 2