SMTL ID : 9s8i.1

Crystal Structure of UDP-N-acetylmuramate-L-alanine ligase (MurC) from Pseudomonas aeruginosa in complex with compound OSA_001176 (WYH78)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x WIR: (1R,2S)-1-({4-[(5-tert-butyl-1-methyl-1H-pyrazol-3-yl)amino]-1H-pyrazolo[3,4-d]pyrimidin-6-yl}amino)-2,3-dihydro-1H-inden-2-ol(Non-covalent)

WIR.1: 16 residues within 4Å: Chain A: H.124, G.125, T.128, T.189, N.190, C.226, Y.246, H.288, L.291, N.292, F.324, A.352, K.355, A.356 Ligands: UNX.5, EDO.6 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.291, A:F.324, A:A.352 Hydrogen bonds: A:T.189, A:N.190, A:N.292, A:N.292 Water bridges: A:T.189, A:N.190 pi-Cation interactions: A:H.288 WIR.18: 16 residues within 4Å: Chain B: H.124, G.125, T.128, T.189, N.190, C.226, Y.246, L.287, H.288, L.291, N.292, F.324, A.352, A.356 Ligands: UNX.22, EDO.23 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.287, B:H.288, B:L.291, B:F.324, B:A.352, B:A.356 Hydrogen bonds: B:T.189, B:N.190, B:N.292, B:N.292 Water bridges: B:T.189, B:K.355 pi-Cation interactions: B:H.288

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

PO4.2: 7 residues within 4Å: Chain A: E.399, V.400, D.412, S.413, R.414, Y.430 Ligands: EDO.10 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.400, A:D.412, A:D.412, A:S.413, A:R.414, A:Y.430 PO4.3: 7 residues within 4Å: Chain A: G.25, A.26, G.27, M.28, S.81, S.82, R.104 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.25, A:A.26, A:G.27, A:M.28, A:S.82 Water bridges: A:G.25 Salt bridges: A:R.104 PO4.4: 4 residues within 4Å: Chain A: H.373, Y.401, A.456, G.457 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.457 Salt bridges: A:H.373 PO4.19: 7 residues within 4Å: Chain B: Y.375, E.399, V.400, D.412, S.413, R.414, Y.430 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.375, B:V.400, B:S.413, B:R.414, B:Y.430 Salt bridges: B:R.414 PO4.20: 4 residues within 4Å: Chain B: H.373, Y.401, A.456, G.457 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.457 Salt bridges: B:H.373 PO4.21: 8 residues within 4Å: Chain B: A.26, G.27, M.28, C.29, G.30, G.150, R.151, L.152 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:C.29, B:G.30, B:L.152, B:L.152

2 x UNX: UNKNOWN LIGAND(Non-functional Binders)

UNX.5: 5 residues within 4Å: Chain A: G.125, K.126, T.127, T.128 Ligands: WIR.1 No protein-ligand interaction detected (PLIP) UNX.22: 5 residues within 4Å: Chain B: G.125, K.126, T.127, T.128 Ligands: WIR.18 No protein-ligand interaction detected (PLIP)

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

EDO.6: 7 residues within 4Å: Chain A: R.323, D.342, Y.343, G.344, E.349, V.353 Ligands: WIR.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.344, A:E.349 EDO.8: 6 residues within 4Å: Chain A: V.227, L.236, T.245, D.251, A.252 Chain B: R.98 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.98, A:T.245 EDO.9: 3 residues within 4Å: Chain A: G.321, R.322, R.323 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.321 EDO.10: 3 residues within 4Å: Chain A: Y.375, P.407 Ligands: PO4.2 No protein-ligand interaction detected (PLIP) EDO.11: 7 residues within 4Å: Chain A: L.108, A.109, M.112, L.167, A.169, L.181 Ligands: EDO.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.112 Water bridges: A:E.170 EDO.12: 5 residues within 4Å: Chain A: L.108, E.170, A.171, D.172 Ligands: EDO.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.172, A:D.172 EDO.13: 5 residues within 4Å: Chain A: R.421, G.424, Q.425, L.426, D.427 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.421, A:G.424, A:L.426 Water bridges: A:Q.425 EDO.15: 7 residues within 4Å: Chain A: N.258, R.260, W.267, F.268, T.269, D.279, V.280 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.258, A:V.280 EDO.23: 6 residues within 4Å: Chain B: R.323, D.342, Y.343, G.344, E.349 Ligands: WIR.18 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.323, B:G.344, B:E.349 EDO.24: 2 residues within 4Å: Chain B: T.243, V.244 2 PLIP interactions: 2 interactions with chain B Water bridges: B:T.243, B:T.243 EDO.25: 4 residues within 4Å: Chain B: R.414, C.417, R.421, Y.430 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.418, B:R.421, B:R.421 Water bridges: B:Y.430 EDO.26: 2 residues within 4Å: Chain B: R.379, D.380 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.379, B:D.380 EDO.27: 9 residues within 4Å: Chain B: L.108, A.109, L.111, M.112, V.147, L.167, A.169, L.181 Ligands: EDO.28 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.112 EDO.28: 6 residues within 4Å: Chain B: E.170, A.171, D.172, D.175, L.181 Ligands: EDO.27 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.172, B:D.172 EDO.29: 6 residues within 4Å: Chain A: R.98 Chain B: V.227, R.233, L.236, T.245, D.251 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.233, B:D.251

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 3 residues within 4Å: Chain A: A.69, P.89, E.96 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.96 PEG.17: 3 residues within 4Å: Chain A: D.302, E.303 Chain B: R.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.302 Water bridges: A:E.303

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

DMS.14: 6 residues within 4Å: Chain A: A.26, G.27, C.29, G.30, R.151, L.152 No protein-ligand interaction detected (PLIP) DMS.16: 1 residues within 4Å: Chain A: N.258 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.258, A:N.258

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Diaz-Saez, L. et al., Crystal Structure of UDP-N-acetylmuramate-L-alanine ligase (MurC) from Pseudomonas aeruginosa in complex with compound OSA_001176 (WYH78). To Be Published

Release Date

2025-09-17

Peptides

UDP-N-acetylmuramate--L-alanine ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

UDP-N-acetylmuramate--L-alanine ligase