SMTL ID : 2wbk.1 (1 other biounit)

Structure of the Michaelis complex of beta-mannosidase, Man2A, provides insight into the conformational itinerary of mannoside hydrolysis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

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

EDO.1: 1 residues within 4Å: Chain A: R.191 Ligand excluded by PLIP EDO.2: 5 residues within 4Å: Chain A: V.347, T.349, Y.352, N.377, L.379 Ligand excluded by PLIP EDO.4: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: W.494, W.500, N.507, D.523, L.524, P.525, M.528 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: I.303, G.304, R.424, N.425, H.426, A.427, R.482 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: Q.205, R.306, D.481, R.482 Ligand excluded by PLIP EDO.9: 8 residues within 4Å: Chain A: I.553, R.572, I.581, P.582, E.583, S.584, F.585, F.588 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: N.312, V.485, H.486, Y.490 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: Q.598, R.601, F.750 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: R.357, R.798, Y.799, S.800, I.815, T.817 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: H.301, R.302, D.382, D.385, N.425, H.426 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: F.17, S.18, Q.19, T.22, K.24, L.43 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: Q.340, L.355, N.623, D.624, I.634, D.635 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain A: S.69, F.70, I.71 Ligand excluded by PLIP EDO.23: 3 residues within 4Å: Chain A: R.351, Y.636, Y.637 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain A: V.270, R.271, M.273, G.278, T.279, T.281 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain A: P.45, N.46, Y.49, N.52 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain A: F.517, E.518, D.578, Q.598, G.599, H.602 Ligand excluded by PLIP EDO.28: 8 residues within 4Å: Chain A: S.18, Q.19, S.20, G.21, T.22, E.23, W.25, E.65 Ligand excluded by PLIP

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

CL.3: 6 residues within 4Å: Chain A: E.440, Y.444, P.489, L.491, A.492, N.493 Ligand excluded by PLIP CL.16: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.29: 4 residues within 4Å: Chain A: Y.337, I.369, G.373, T.374 Ligand excluded by PLIP CL.30: 1 residues within 4Å: Chain A: E.53 Ligand excluded by PLIP

1 x M2F: 2,4-dinitrophenyl 2-deoxy-2-fluoro-beta-D-mannopyranoside(Non-covalent)

M2F.5: 14 residues within 4Å: Chain A: N.153, W.173, D.174, W.175, W.370, C.399, N.436, E.437, W.445, W.508, Y.512, Q.530, W.620, W.631 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.445, A:Y.512 Hydrogen bonds: A:W.173, A:W.173, A:W.370, A:Y.512 pi-Stacking: A:W.508 Halogen bonds: A:N.436

6 x BR: BROMIDE ION(Non-covalent)

BR.17: 4 residues within 4Å: Chain A: G.81, I.82, P.115, K.117 Ligand excluded by PLIP BR.18: 2 residues within 4Å: Chain A: Q.83, P.115 Ligand excluded by PLIP BR.19: 4 residues within 4Å: Chain A: Q.660, Q.661, N.662, D.663 Ligand excluded by PLIP BR.20: 3 residues within 4Å: Chain A: F.451, T.452, V.455 Ligand excluded by PLIP BR.21: 1 residues within 4Å: Chain A: Y.484 Ligand excluded by PLIP BR.26: 2 residues within 4Å: Chain A: R.186, N.377 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Offen, W.A. et al., Structure of the Michaelis Complex of Beta-Mannosidase, Man2A, Provides Insight Into the Conformational Itinerary of Mannoside Hydrolysis. Cell(Cambridge,Mass.) (2009)

Release Date

2009-03-17

Peptides

BETA-MANNOSIDASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

BETA-MANNOSIDASE

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