SMTL ID : 7op7.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

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

EDO.1: 8 residues within 4Å: Chain A: W.496, W.502, S.507, N.509, D.525, L.526, P.527, M.530 Ligand excluded by PLIP EDO.2: 9 residues within 4Å: Chain A: S.20, Q.21, S.22, G.23, T.24, E.25, W.27, E.67 Ligands: CL.29 Ligand excluded by PLIP EDO.3: 5 residues within 4Å: Chain A: Q.207, R.308, D.483, R.484 Ligands: EDO.7 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: Q.342, N.625, D.626, I.636, D.637, Y.638 Ligand excluded by PLIP EDO.5: 8 residues within 4Å: Chain A: F.333, R.610, R.613, I.672, S.673, D.674, N.710, T.711 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: I.305, G.306, R.426, N.427, H.428, A.429, R.484 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: Q.207, T.309, D.483 Ligands: EDO.3 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: R.353, Y.638, Y.639 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: V.419, Y.420, R.423 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: F.519, D.580, Y.581, Q.600, G.601 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: V.349, T.351, Y.354, N.379, L.381 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: Q.772, R.822, I.823, K.824, E.827, E.828 Ligand excluded by PLIP EDO.32: 8 residues within 4Å: Chain A: W.175, W.372, C.401, N.438, E.439, E.532, W.622 Ligands: VEE.13 Ligand excluded by PLIP EDO.33: 3 residues within 4Å: Chain A: N.314, H.488, Y.492 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain A: D.692, S.784, M.785 Ligand excluded by PLIP EDO.35: 4 residues within 4Å: Chain A: C.714, V.715, Y.716, R.717 Ligand excluded by PLIP EDO.36: 3 residues within 4Å: Chain A: S.71, E.126, H.128 Ligand excluded by PLIP

1 x VEE: (1R,2S,3R,4S,5R,6R)-5-(8-azidooctylamino)-6-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol(Covalent)

VEE.13: 14 residues within 4Å: Chain A: W.175, D.176, W.177, W.372, C.401, N.438, E.439, W.496, W.510, Y.514, E.532, W.622, W.633 Ligands: EDO.32 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.510, A:Y.514 Hydrogen bonds: A:W.175, A:W.372, A:N.438, A:Y.514

6 x BR: BROMIDE ION(Non-covalent)

BR.14: 3 residues within 4Å: Chain A: I.84, P.117, K.119 Ligand excluded by PLIP BR.15: 3 residues within 4Å: Chain A: P.474, Y.486, H.488 Ligand excluded by PLIP BR.16: 2 residues within 4Å: Chain A: Q.85, P.117 Ligand excluded by PLIP BR.17: 3 residues within 4Å: Chain A: Q.662, N.664, D.665 Ligand excluded by PLIP BR.18: 3 residues within 4Å: Chain A: F.453, T.454, V.457 Ligand excluded by PLIP BR.19: 2 residues within 4Å: Chain A: P.189, N.379 Ligand excluded by PLIP

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

CL.20: 1 residues within 4Å: Chain A: H.303 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain A: V.656, R.675 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain A: N.277, W.279, N.367 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain A: N.260, H.261 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain A: Q.745, V.746, A.747 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain A: T.211, D.212 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain A: K.698, K.699 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain A: L.796, Q.797, R.822 Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain A: T.454, P.455, E.456 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain A: E.25, W.27 Ligands: EDO.2 Ligand excluded by PLIP CL.30: 2 residues within 4Å: Chain A: G.258, I.259 Ligand excluded by PLIP CL.31: 2 residues within 4Å: Chain A: K.106, H.134 Ligand excluded by PLIP

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

2022-02-02

Peptides

Beta-mannosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Beta-mannosidase

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