SMTL ID : 9auz.1

Crystal structure of S. aureus GuaB dCBS with inhibitor GNE9979

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-tetramer

Ligands

4 x IMP: INOSINIC ACID(Non-covalent)

IMP.1: 22 residues within 4Å: Chain A: A.64, M.66, N.168, G.193, S.194, I.195, C.196, T.198, D.229, G.230, G.231, M.250, L.251, G.252, S.253, Y.276, G.278, M.279, G.280, E.306, G.307 Ligands: VP4.2 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:N.168, A:S.194, A:T.198, A:D.229, A:D.229, A:G.231, A:I.232, A:G.252, A:S.253, A:M.279, A:G.280, A:E.306 Water bridges: A:G.65, A:K.187, A:G.191, A:G.193, A:G.230, A:G.230 IMP.3: 22 residues within 4Å: Chain B: A.64, M.66, N.168, G.193, S.194, I.195, C.196, T.198, D.229, G.230, G.231, M.250, L.251, G.252, S.253, Y.276, G.278, M.279, G.280, E.306, G.307 Ligands: VP4.4 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:N.168, B:S.194, B:T.198, B:D.229, B:D.229, B:G.231, B:I.232, B:G.252, B:S.253, B:M.279, B:G.280, B:E.306 Water bridges: B:G.65, B:K.187, B:G.191, B:G.193, B:G.230, B:G.230 IMP.5: 22 residues within 4Å: Chain C: A.64, M.66, N.168, G.193, S.194, I.195, C.196, T.198, D.229, G.230, G.231, M.250, L.251, G.252, S.253, Y.276, G.278, M.279, G.280, E.306, G.307 Ligands: VP4.6 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:N.168, C:S.194, C:T.198, C:D.229, C:D.229, C:G.231, C:I.232, C:G.252, C:S.253, C:M.279, C:G.280, C:E.306 Water bridges: C:G.65, C:K.187, C:G.191, C:G.193, C:G.230, C:G.230 IMP.7: 22 residues within 4Å: Chain D: A.64, M.66, N.168, G.193, S.194, I.195, C.196, T.198, D.229, G.230, G.231, M.250, L.251, G.252, S.253, Y.276, G.278, M.279, G.280, E.306, G.307 Ligands: VP4.8 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:N.168, D:S.194, D:T.198, D:D.229, D:D.229, D:G.231, D:I.232, D:G.252, D:S.253, D:M.279, D:G.280, D:E.306 Water bridges: D:G.65, D:K.187, D:G.191, D:G.193, D:G.230, D:G.230

4 x VP4: N-[4-chloro-3-(dimethylamino)phenyl]-N~2~-[3-(hydroxymethyl)quinolin-6-yl]-L-alaninamide(Non-covalent)

VP4.2: 17 residues within 4Å: Chain A: A.141, H.142, G.189, I.190, G.191, T.198, M.279, G.280, F.303, V.304, E.306 Chain D: L.41, P.42, A.331, G.334, Y.335 Ligands: IMP.1 9 PLIP interactions: 2 interactions with chain D, 7 interactions with chain A Hydrophobic interactions: D:Y.335, A:A.141, A:M.279, A:F.303 Hydrogen bonds: D:Y.335, A:G.189, A:G.191, A:E.306 Water bridges: A:A.141 VP4.4: 17 residues within 4Å: Chain B: A.141, H.142, G.189, I.190, G.191, T.198, M.279, G.280, F.303, V.304, E.306 Chain C: L.41, P.42, A.331, G.334, Y.335 Ligands: IMP.3 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:A.141, B:M.279, B:F.303, C:Y.335 Hydrogen bonds: B:G.189, B:G.191, B:E.306, C:Y.335 Water bridges: B:A.141 VP4.6: 17 residues within 4Å: Chain A: L.41, P.42, A.331, G.334, Y.335 Chain C: A.141, H.142, G.189, I.190, G.191, T.198, M.279, G.280, F.303, V.304, E.306 Ligands: IMP.5 9 PLIP interactions: 2 interactions with chain A, 7 interactions with chain C Hydrophobic interactions: A:Y.335, C:A.141, C:M.279, C:F.303 Hydrogen bonds: A:Y.335, C:G.189, C:G.191, C:E.306 Water bridges: C:A.141 VP4.8: 17 residues within 4Å: Chain B: L.41, P.42, A.331, G.334, Y.335 Chain D: A.141, H.142, G.189, I.190, G.191, T.198, M.279, G.280, F.303, V.304, E.306 Ligands: IMP.7 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:A.141, D:M.279, D:F.303, B:Y.335 Hydrogen bonds: D:G.189, D:G.191, D:E.306, B:Y.335 Water bridges: D:A.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kofoed, E.M. et al., Discovery of GuaB inhibitors with efficacy against Acinetobacter baumannii infection. Mbio (2024)

Release Date

2025-01-15

Peptides

Inosine-5'-monophosphate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Inosine-5'-monophosphate dehydrogenase

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