SMTL ID : 7op6.2 (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

1 x JIT: beta-D-manno-configured cyclophellitol aziridine(Non-covalent)

JIT.1: 13 residues within 4Å: Chain A: W.175, D.176, W.177, W.372, C.401, N.438, E.439, W.510, Y.514, E.532, W.622, W.633 Ligands: VKH.32 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.438, A:E.439, A:Y.514, A:E.532 Water bridges: A:D.176, A:D.176

4 x BR: BROMIDE ION(Non-covalent)

BR.2: 4 residues within 4Å: Chain A: G.83, I.84, P.117, K.119 Ligand excluded by PLIP BR.3: 1 residues within 4Å: Chain A: Y.486 Ligand excluded by PLIP BR.4: 3 residues within 4Å: Chain A: Q.662, N.664, D.665 Ligand excluded by PLIP BR.5: 2 residues within 4Å: Chain A: P.189, N.379 Ligand excluded by PLIP

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

EDO.6: 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.7: 7 residues within 4Å: Chain A: F.19, S.20, Q.21, K.26, W.27, M.28, L.45 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: F.519, E.520, D.580, Q.600, G.601, H.604 Ligand excluded by PLIP EDO.9: 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.10: 2 residues within 4Å: Chain A: Y.324, M.617 Ligand excluded by PLIP EDO.11: 8 residues within 4Å: Chain A: E.442, K.445, Y.446, P.491, Y.492, L.493, A.494, N.495 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: S.20, Q.21, S.22, G.23, T.24, E.25, E.67 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: Q.662, F.752, F.753 Ligands: CL.27 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: D.65, H.134, R.138, Q.139 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: N.314, V.487, H.488, Y.492 Ligand excluded by PLIP EDO.16: 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.17: 2 residues within 4Å: Chain A: L.103, K.106 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: Q.207, L.208, T.309, D.483 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: D.96, K.106, H.134, Q.139 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain A: R.353, Y.638, Y.639 Ligand excluded by PLIP EDO.21: 7 residues within 4Å: Chain A: Q.342, L.357, N.625, D.626, I.636, D.637, Y.638 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain A: V.419, Y.420, R.423 Ligand excluded by PLIP

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

CL.23: 2 residues within 4Å: Chain A: F.485, Y.486 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain A: G.52, M.53 Ligand excluded by PLIP CL.25: 3 residues within 4Å: Chain A: F.453, T.454, V.457 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain A: Q.554, I.555 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain A: F.752 Ligands: EDO.13 Ligand excluded by PLIP CL.28: 2 residues within 4Å: Chain A: K.713, C.714 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain A: Q.85, T.115, P.117 Ligand excluded by PLIP CL.30: 2 residues within 4Å: Chain A: K.26, W.27 Ligand excluded by PLIP

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

NA.31: 4 residues within 4Å: Chain A: Q.745, V.746, A.747, E.748 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.746, A:E.748

1 x VKH: (1~{R},2~{R},3~{S},4~{R},5~{R},6~{R})-5-(hydroxymethyl)-7-azabicyclo[4.1.0]heptane-2,3,4-triol(Non-covalent)

VKH.32: 11 residues within 4Å: Chain A: W.175, D.176, W.177, C.401, E.439, W.510, Y.514, E.532, W.622, W.633 Ligands: JIT.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.514, A:Y.514 Water bridges: A:D.176

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
B

Beta-mannosidase

Related Entries With Identical Sequence