SMTL ID : 2vl4.2 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

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

MNM.1: 13 residues within 4Å: Chain A: W.173, D.174, W.175, W.370, C.399, N.436, E.437, W.508, Y.512, E.530, W.620, W.631 Ligands: EDO.15 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:W.173, A:W.370, A:W.370, A:N.436, A:Y.512, A:Y.512, A:E.530

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

EDO.2: 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.3: 4 residues within 4Å: Chain A: Y.322, P.329, P.612, M.615 Ligand excluded by PLIP EDO.4: 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.5: 3 residues within 4Å: Chain A: R.351, Y.636, Y.637 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: F.17, S.18, Q.19, T.22, K.24, M.26 Ligand excluded by PLIP EDO.7: 8 residues within 4Å: Chain A: F.331, R.608, R.611, I.670, S.671, D.672, N.708, T.709 Ligand excluded by PLIP EDO.8: 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.9: 6 residues within 4Å: Chain A: H.301, R.302, D.382, D.385, N.425, H.426 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: W.494, W.508, Y.512 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: H.749, F.750 Ligands: EDO.24 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: N.312, V.485, H.486, Y.490 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: D.63, H.132, R.136, Q.137 Ligand excluded by PLIP EDO.14: 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.15: 7 residues within 4Å: Chain A: N.153, W.173, D.174, C.399, E.437, W.445 Ligands: MNM.1 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain A: N.275, W.277, M.330, F.331, K.333, N.365, D.672 Ligand excluded by PLIP EDO.21: 2 residues within 4Å: Chain A: R.67, Y.128 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain A: R.357, R.798, Y.799, S.800, I.815, T.817 Ligand excluded by PLIP EDO.24: 8 residues within 4Å: Chain A: Q.660, H.749, F.750, F.751, R.752, K.753 Ligands: EDO.11, CL.22 Ligand excluded by PLIP EDO.25: 2 residues within 4Å: Chain A: K.117, S.118 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain A: V.347, T.349, Y.352, N.377, L.379 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain A: C.712, V.713, Y.714, R.715 Ligand excluded by PLIP

4 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: 3 residues within 4Å: Chain A: Q.660, N.662, D.663 Ligand excluded by PLIP BR.19: 2 residues within 4Å: Chain A: P.472, Y.484 Ligand excluded by PLIP BR.20: 2 residues within 4Å: Chain A: Q.83, P.115 Ligand excluded by PLIP

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

CL.22: 6 residues within 4Å: Chain A: H.602, P.658, I.659, Q.660, H.749 Ligands: EDO.24 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain A: Q.205, S.207, T.307 Ligand excluded by PLIP CL.29: 1 residues within 4Å: Chain A: D.772 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
B

BETA-MANNOSIDASE

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