SMTL ID : 7op6.1 (1 other biounit)

Bacteroides thetaiotaomicron mannosidase GH2 with beta-manno-configured cyclophellitol aziridine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

6 x BR: BROMIDE ION(Non-covalent)

BR.1: 2 residues within 4Å: Chain A: Q.85, P.117 Ligand excluded by PLIP BR.2: 3 residues within 4Å: Chain A: R.188, P.189, N.379 Ligand excluded by PLIP BR.3: 3 residues within 4Å: Chain A: I.84, P.117, K.119 Ligand excluded by PLIP BR.4: 1 residues within 4Å: Chain A: Y.486 Ligand excluded by PLIP BR.5: 2 residues within 4Å: Chain A: N.260, H.261 Ligand excluded by PLIP BR.6: 2 residues within 4Å: Chain A: Q.662, D.665 Ligand excluded by PLIP

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

EDO.7: 5 residues within 4Å: Chain A: Q.207, R.308, D.483, R.484 Ligands: EDO.17 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.308, A:R.308 Water bridges: A:I.310 EDO.8: 7 residues within 4Å: Chain A: I.305, G.306, R.426, N.427, H.428, A.429, R.484 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.306, A:G.306, A:R.484 Water bridges: A:R.308, A:A.429 EDO.9: 8 residues within 4Å: Chain A: W.496, W.502, S.507, N.509, D.525, L.526, P.527, M.530 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.509, A:N.509, A:L.526 EDO.10: 7 residues within 4Å: Chain A: F.19, S.20, Q.21, T.24, K.26, M.28, L.45 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.21, A:T.24, A:K.26 EDO.11: 4 residues within 4Å: Chain A: N.314, V.487, H.488, Y.492 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.314, A:H.488 Water bridges: A:Y.492 EDO.12: 4 residues within 4Å: Chain A: Q.745, V.746, A.747, E.748 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.745, A:E.748, A:E.748 Water bridges: A:E.748 EDO.13: 3 residues within 4Å: Chain A: D.65, H.134, R.138 No protein-ligand interaction detected (PLIP) EDO.14: 6 residues within 4Å: Chain A: Q.342, N.625, D.626, I.636, D.637, Y.638 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.625, A:D.626, A:D.637 EDO.15: 7 residues within 4Å: Chain A: S.20, Q.21, S.22, G.23, T.24, E.25, E.67 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.20, A:S.20, A:G.23, A:T.24, A:E.25 EDO.16: 5 residues within 4Å: Chain A: D.580, Y.581, Q.600, K.755, T.756 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.581, A:T.756, A:T.756 EDO.17: 4 residues within 4Å: Chain A: Q.207, S.209, D.483 Ligands: EDO.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.207, A:D.483, A:D.483 Water bridges: A:R.308 EDO.18: 3 residues within 4Å: Chain A: I.330, P.331, N.710 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.710 EDO.19: 3 residues within 4Å: Chain A: V.419, Y.420, R.423 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.423 Water bridges: A:S.201, A:D.202, A:Y.420 EDO.20: 1 residues within 4Å: Chain A: H.261 No protein-ligand interaction detected (PLIP) EDO.21: 2 residues within 4Å: Chain A: E.479, F.480 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.415

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

CL.22: 3 residues within 4Å: Chain A: F.453, T.454, V.457 Ligand excluded by PLIP CL.23: 3 residues within 4Å: Chain A: P.763, T.764, E.838 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain A: N.277, W.279, N.367 Ligand excluded by PLIP CL.25: 1 residues within 4Å: Chain A: F.752 Ligand excluded by PLIP CL.26: 4 residues within 4Å: Chain A: A.233, E.234, A.292, G.294 Ligand excluded by PLIP CL.27: 1 residues within 4Å: Chain A: Q.554 Ligand excluded by PLIP

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

NA.28: 3 residues within 4Å: Chain A: E.89, N.380, Y.420 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.89, A:N.380 Water bridges: A:R.188, A:R.424 NA.29: 5 residues within 4Å: Chain A: F.333, R.610, R.613, I.672, D.674 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.610, A:R.613, A:D.674

1 x JIW: beta-D-manno-configured cyclophellitol aziridine, reacted form(Covalent)

JIW.30: 8 residues within 4Å: Chain A: W.175, D.176, C.401, N.438, E.439, W.510, E.532, W.622 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:E.532 Hydrogen bonds: A:W.175, A:N.438, A:E.439, A:E.532, A:E.532

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McGregor, N.G.S. et al., Synthesis of broad-specificity activity-based probes for exo -beta-mannosidases. Org.Biomol.Chem. (2022)

Release Date

2022-05-18

Peptides

Beta-mannosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-mannosidase

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