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

Structural and biochemical evidence for a boat-like transition state in beta-mannosidases

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: Y.322, P.329, R.611, M.615 Ligand excluded by PLIP EDO.3: 3 residues within 4Å: Chain A: N.268, P.269, V.270 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: Q.340, L.355, N.623, D.624, I.634, D.635, Y.636 Ligand excluded by PLIP EDO.5: 8 residues within 4Å: Chain A: W.494, W.500, S.505, N.507, D.523, L.524, P.525, M.528 Ligand excluded by PLIP EDO.6: 8 residues within 4Å: Chain A: I.303, G.304, R.306, R.424, N.425, H.426, A.427, R.482 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: Q.205, R.306, D.481, R.482 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: E.440, K.443, Y.444, P.489, L.491, A.492, N.493 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: I.553, 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: 5 residues within 4Å: Chain A: Q.598, R.601, H.749, F.750 Ligands: EDO.17 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: V.417, Y.418, R.421 Ligand excluded by PLIP EDO.13: 9 residues within 4Å: Chain A: Y.92, A.93, D.94, K.104, A.105, D.106, H.132 Ligands: EDO.29, EDO.36 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: R.798, Y.799, S.800, I.815, T.817 Ligand excluded by PLIP EDO.15: 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 EDO.16: 5 residues within 4Å: Chain A: R.601, Q.646, R.649, S.747, V.748 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain A: D.578, Y.579, Q.598, K.753, T.754 Ligands: EDO.11 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain A: S.18, Q.19, T.22, K.24, M.26, L.38, L.43 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain A: V.347, T.349, Y.352, N.377, L.379 Ligand excluded by PLIP EDO.23: 3 residues within 4Å: Chain A: D.63, H.132, R.136 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain A: W.494, W.508, Y.512 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain A: Y.92, D.106, Q.137, R.411 Ligands: EDO.13 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain A: K.515, S.519, D.523 Ligand excluded by PLIP EDO.35: 5 residues within 4Å: Chain A: Y.444, W.445, N.493, W.494, G.495 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain A: D.94, K.104, H.132, Q.137 Ligands: EDO.13 Ligand excluded by PLIP EDO.37: 5 residues within 4Å: Chain A: P.761, T.762, H.833, R.835, E.836 Ligand excluded by PLIP EDO.38: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.39: 10 residues within 4Å: Chain A: P.47, F.48, Y.49, G.50, M.51, N.52, E.53, A.560, H.561, W.626 Ligand excluded by PLIP

1 x NOY: (2R,3S,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE-2,3,4-TRIOL(Non-covalent)

NOY.2: 10 residues within 4Å: Chain A: W.173, D.174, W.175, W.370, N.436, E.437, W.508, Y.512, E.530, W.631 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.508 Hydrogen bonds: A:W.173, A:W.370, A:N.436, A:Y.512, A:E.530 Water bridges: A:W.175, A:W.370, A:Y.512

7 x BR: BROMIDE ION(Non-covalent)

BR.20: 5 residues within 4Å: Chain A: G.81, I.82, P.115, V.116, K.117 Ligand excluded by PLIP BR.21: 2 residues within 4Å: Chain A: N.258, H.259 Ligand excluded by PLIP BR.22: 2 residues within 4Å: Chain A: F.467, Y.484 Ligand excluded by PLIP BR.26: 2 residues within 4Å: Chain A: R.186, N.377 Ligand excluded by PLIP BR.30: 3 residues within 4Å: Chain A: N.275, W.277, N.365 Ligand excluded by PLIP BR.31: 2 residues within 4Å: Chain A: Q.83, P.115 Ligand excluded by PLIP BR.32: 3 residues within 4Å: Chain A: Q.660, N.662, D.663 Ligand excluded by PLIP

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

CL.24: 5 residues within 4Å: Chain A: H.602, P.658, I.659, Q.660, H.749 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain A: F.451, T.452, V.455 Ligand excluded by PLIP CL.28: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.33: 3 residues within 4Å: Chain A: H.301, N.425, H.426 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tailford, L.E. et al., Structural and Biochemical Evidence for a Boat-Like Transition State in Beta-Mannosidases. Nat.Chem.Biol. (2008)

Release Date

2008-04-01

Peptides

BETA-MANNOSIDASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

BETA-MANNOSIDASE

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