SMTL ID : 7fe3.1

Crystal structure of GH65 alpha-1,2-glucosidase from Flavobacterium johnsoniae

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

homo-hexamer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: R.71, M.327, G.333, Y.334, N.619 Ligand excluded by PLIP EDO.2: 5 residues within 4Å: Chain A: P.326, Y.334, F.339, D.341, F.622 Ligand excluded by PLIP EDO.3: 9 residues within 4Å: Chain A: R.71, Y.334, W.388, E.389, T.398, P.399, A.402, T.404 Ligands: EDO.4 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: R.71, G.72, P.399, N.401 Ligands: EDO.3 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: H.20, L.26, S.27, Q.303, P.607, R.609 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: D.304, S.307, M.308, F.608, R.609, I.611, Y.621 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: V.400, A.402, L.403, G.405, A.406 Chain B: R.264, I.267 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: L.206, D.208, S.242, F.243, A.244, K.274 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: Y.334, K.535, D.570, P.572, E.613, C.614 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: Y.172, V.189, Y.259 Chain F: Q.170 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain B: P.326, Y.334, F.339, D.341, F.622 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain B: R.71, G.333, Y.334, E.613, N.619 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain B: L.206, D.208, S.242, F.243, A.244, K.274 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain B: N.167, N.168, Q.169 Chain D: P.193 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain B: D.22, P.23, W.24, K.25, R.110 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain B: H.20, L.26, S.27, Q.303, P.607, R.609 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain C: P.326, Y.334, F.339, D.341, F.622 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain C: R.71, G.333, Y.334, N.619 Ligand excluded by PLIP EDO.19: 8 residues within 4Å: Chain C: R.71, Y.334, W.388, E.389, T.398, P.399, A.402, T.404 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain C: H.20, L.26, S.27, Q.303, P.607, F.608, R.609 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain C: R.71, G.72, P.399, N.401 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain C: L.206, D.208, S.242, F.243, A.244, K.274 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain C: D.304, S.307, M.308, R.609, I.611, Y.621 Ligand excluded by PLIP EDO.24: 7 residues within 4Å: Chain A: R.264, I.267 Chain C: V.400, A.402, L.403, G.405, A.406 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain C: S.569, D.570, C.614, K.615 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain C: S.33, N.34, N.35, Y.36, Y.37 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain D: R.71, M.327, G.333, Y.334, N.619 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain D: P.326, Y.334, F.339, D.341, F.622 Ligand excluded by PLIP EDO.29: 9 residues within 4Å: Chain D: R.71, Y.334, W.388, E.389, T.398, P.399, A.402, T.404 Ligands: EDO.30 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain D: R.71, G.72, P.399, N.401 Ligands: EDO.29 Ligand excluded by PLIP EDO.31: 6 residues within 4Å: Chain D: H.20, L.26, S.27, Q.303, P.607, R.609 Ligand excluded by PLIP EDO.32: 7 residues within 4Å: Chain D: D.304, S.307, M.308, F.608, R.609, I.611, Y.621 Ligand excluded by PLIP EDO.33: 7 residues within 4Å: Chain D: V.400, A.402, L.403, G.405, A.406 Chain E: R.264, I.267 Ligand excluded by PLIP EDO.34: 6 residues within 4Å: Chain D: L.206, D.208, S.242, F.243, A.244, K.274 Ligand excluded by PLIP EDO.35: 6 residues within 4Å: Chain D: Y.334, K.535, D.570, P.572, E.613, C.614 Ligand excluded by PLIP EDO.36: 4 residues within 4Å: Chain C: Q.170 Chain D: Y.172, V.189, Y.259 Ligand excluded by PLIP EDO.37: 5 residues within 4Å: Chain E: P.326, Y.334, F.339, D.341, F.622 Ligand excluded by PLIP EDO.38: 5 residues within 4Å: Chain E: R.71, G.333, Y.334, E.613, N.619 Ligand excluded by PLIP EDO.39: 6 residues within 4Å: Chain E: L.206, D.208, S.242, F.243, A.244, K.274 Ligand excluded by PLIP EDO.40: 4 residues within 4Å: Chain A: P.193 Chain E: N.167, N.168, Q.169 Ligand excluded by PLIP EDO.41: 5 residues within 4Å: Chain E: D.22, P.23, W.24, K.25, R.110 Ligand excluded by PLIP EDO.42: 6 residues within 4Å: Chain E: H.20, L.26, S.27, Q.303, P.607, R.609 Ligand excluded by PLIP EDO.43: 5 residues within 4Å: Chain F: P.326, Y.334, F.339, D.341, F.622 Ligand excluded by PLIP EDO.44: 4 residues within 4Å: Chain F: R.71, G.333, Y.334, N.619 Ligand excluded by PLIP EDO.45: 8 residues within 4Å: Chain F: R.71, Y.334, W.388, E.389, T.398, P.399, A.402, T.404 Ligand excluded by PLIP EDO.46: 7 residues within 4Å: Chain F: H.20, L.26, S.27, Q.303, P.607, F.608, R.609 Ligand excluded by PLIP EDO.47: 4 residues within 4Å: Chain F: R.71, G.72, P.399, N.401 Ligand excluded by PLIP EDO.48: 6 residues within 4Å: Chain F: L.206, D.208, S.242, F.243, A.244, K.274 Ligand excluded by PLIP EDO.49: 6 residues within 4Å: Chain F: D.304, S.307, M.308, R.609, I.611, Y.621 Ligand excluded by PLIP EDO.50: 7 residues within 4Å: Chain D: R.264, I.267 Chain F: V.400, A.402, L.403, G.405, A.406 Ligand excluded by PLIP EDO.51: 4 residues within 4Å: Chain F: S.569, D.570, C.614, K.615 Ligand excluded by PLIP EDO.52: 5 residues within 4Å: Chain F: S.33, N.34, N.35, Y.36, Y.37 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakamura, S. et al., Structure of a bacterial alpha-1,2-glucosidase defines mechanisms of hydrolysis and substrate specificity in GH65 family hydrolases. J.Biol.Chem. (2021)

Release Date

2021-11-10

Peptides

Candidate alpha glycoside phosphorylase Glycoside hydrolase family 65: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Candidate alpha glycoside phosphorylase Glycoside hydrolase family 65

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