SMTL ID : 8e72.1

Treponema lecithinolyticum beta-glucuronidase in complex with a ciprofloxacin-glucuronide conjugate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

4 x USL: 3-carboxy-1-cyclopropyl-6-fluoro-7-(4-beta-D-glucopyranuronosyl-3,4-dihydropyrazin-1(2H)-yl)-4-oxo-1,4-dihydroquinoline(Non-covalent)(Covalent)

USL.1: 19 residues within 4Å: Chain A: L.175, D.194, H.360, N.444, E.445, L.479, N.499, Y.501, Y.505, E.536, W.581, F.586, I.593, R.594, N.598, K.600 Chain C: F.179, F.180, L.592 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:L.175, A:Y.505, C:F.179 Hydrogen bonds: A:D.194, A:D.194, A:N.444, A:E.445, A:N.499, A:W.581, A:N.598 Water bridges: A:H.360 Salt bridges: A:R.594, A:K.600 pi-Stacking: A:Y.505 USL.3: 19 residues within 4Å: Chain B: D.194, H.360, F.391, N.444, E.445, L.479, N.499, Y.501, Y.505, E.536, W.581, F.586, I.593, R.594, N.598, K.600 Chain D: F.179, F.180, L.592 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:I.593, D:F.179, D:F.180 Hydrogen bonds: B:D.194, B:N.444, B:E.445, B:N.499, B:W.581, B:N.598 Water bridges: B:H.360, B:E.445 Salt bridges: B:R.594, B:K.600 pi-Stacking: B:Y.505, B:Y.505 USL.7: 19 residues within 4Å: Chain A: F.179, F.180, L.592 Chain C: L.175, D.194, H.360, N.444, E.445, L.479, N.499, Y.501, Y.505, E.536, W.581, F.586, I.593, R.594, N.598, K.600 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.175, C:Y.505, A:F.179 Hydrogen bonds: C:D.194, C:N.444, C:E.445, C:N.499, C:Y.501, C:Y.505, C:W.581, C:N.598 Water bridges: C:H.360, C:E.445 Salt bridges: C:R.594, C:K.600 pi-Stacking: C:Y.505 USL.9: 19 residues within 4Å: Chain B: F.179, F.180, L.592 Chain D: D.194, H.360, F.391, N.444, E.445, L.479, N.499, Y.501, Y.505, E.536, W.581, F.586, I.593, R.594, N.598, K.600 17 PLIP interactions: 15 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:I.593, B:F.179, B:F.180 Hydrogen bonds: D:D.194, D:D.194, D:N.444, D:E.445, D:N.499, D:Y.501, D:Y.505, D:W.581, D:N.598 Water bridges: D:H.360 Salt bridges: D:R.594, D:K.600 pi-Stacking: D:Y.505, D:Y.505

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: A.242, H.243, G.291 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.243, A:G.291 Water bridges: A:H.243, A:G.291 Salt bridges: A:H.243 SO4.4: 3 residues within 4Å: Chain B: Y.86, R.158, K.187 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.86 Salt bridges: B:R.158, B:K.187 SO4.5: 6 residues within 4Å: Chain B: A.242, H.243, T.244, N.261, T.262, G.263 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.244, B:N.261, B:G.263 Salt bridges: B:H.243 SO4.6: 2 residues within 4Å: Chain B: R.146, D.147 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.147, B:D.147, B:D.147 SO4.8: 3 residues within 4Å: Chain C: A.242, H.243, G.291 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:H.243, C:G.291 Water bridges: C:H.243, C:G.291 Salt bridges: C:H.243 SO4.10: 3 residues within 4Å: Chain D: Y.86, R.158, K.187 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Y.86, D:Y.86 Salt bridges: D:R.158, D:K.187 SO4.11: 6 residues within 4Å: Chain D: A.242, H.243, T.244, N.261, T.262, G.263 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.244, D:T.244, D:N.261, D:G.263 Salt bridges: D:H.243 SO4.12: 2 residues within 4Å: Chain D: R.146, D.147 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.147, D:D.147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lietzan, A.D. et al., Microbial beta-glucuronidases drive human periodontal disease etiology. Sci Adv (2023)

Release Date

2023-06-21

Peptides

Glycosyl hydrolase family 2, TIM barrel domain protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Glycosyl hydrolase family 2, TIM barrel domain protein