SMTL ID : 5zn6.1 (1 other biounit)

Crystal structure of GH31 alpha-xylosidase from a soil metagenome

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

31 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 12 residues within 4Å: Chain A: L.252, D.280, F.281, W.319, W.386, D.388, E.389, W.455, D.458, F.491, H.521 Ligands: GOL.3 Ligand excluded by PLIP GOL.2: 6 residues within 4Å: Chain A: F.351, D.492, F.523, M.542 Chain C: R.100 Ligands: GOL.3 Ligand excluded by PLIP GOL.3: 9 residues within 4Å: Chain A: N.170, F.351, E.389, E.393, R.441, D.458 Chain C: R.100 Ligands: GOL.1, GOL.2 Ligand excluded by PLIP GOL.4: 8 residues within 4Å: Chain A: R.467, D.607, P.619, V.620, L.621, E.622, Q.625, R.628 Ligand excluded by PLIP GOL.5: 4 residues within 4Å: Chain A: S.627, D.654, C.655, D.656 Ligand excluded by PLIP GOL.6: 5 residues within 4Å: Chain A: P.499, A.500, E.503, G.624, R.626 Ligand excluded by PLIP GOL.7: 7 residues within 4Å: Chain A: T.361, R.366, L.406, I.415, R.418, G.419, Q.422 Ligand excluded by PLIP GOL.8: 8 residues within 4Å: Chain A: Q.510, F.514, L.566, L.641, N.642, A.661, I.662, V.664 Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain A: Y.96, H.119, R.137, V.202, T.204 Ligand excluded by PLIP GOL.10: 9 residues within 4Å: Chain B: N.170, F.351, E.389, E.393, R.441, D.458 Chain D: R.100 Ligands: GOL.13, GOL.16 Ligand excluded by PLIP GOL.11: 6 residues within 4Å: Chain B: Y.152, Q.153, Q.154, Q.172 Chain D: Y.96, L.117 Ligand excluded by PLIP GOL.12: 7 residues within 4Å: Chain B: T.361, R.366, L.406, I.415, R.418, G.419, Q.422 Ligand excluded by PLIP GOL.13: 12 residues within 4Å: Chain B: L.252, D.280, F.281, W.319, W.386, D.388, E.389, W.455, D.458, F.491, H.521 Ligands: GOL.10 Ligand excluded by PLIP GOL.14: 6 residues within 4Å: Chain A: G.130, K.131, F.132 Chain B: R.403, G.407, P.408 Ligand excluded by PLIP GOL.15: 8 residues within 4Å: Chain B: R.467, D.607, P.619, V.620, L.621, E.622, Q.625, R.628 Ligand excluded by PLIP GOL.16: 6 residues within 4Å: Chain B: F.351, D.492, F.523, M.542 Chain D: R.100 Ligands: GOL.10 Ligand excluded by PLIP GOL.17: 7 residues within 4Å: Chain B: R.100 Chain D: F.351, F.491, D.492, F.523, M.542 Ligands: GOL.26 Ligand excluded by PLIP GOL.18: 12 residues within 4Å: Chain C: L.252, D.280, F.281, W.319, W.386, D.388, E.389, W.455, D.458, F.491, H.521 Ligands: GOL.19 Ligand excluded by PLIP GOL.19: 9 residues within 4Å: Chain A: R.100 Chain C: N.170, F.351, E.389, E.393, R.441, D.458 Ligands: GOL.18, GOL.25 Ligand excluded by PLIP GOL.20: 3 residues within 4Å: Chain C: V.75, Y.85, G.89 Ligand excluded by PLIP GOL.21: 7 residues within 4Å: Chain C: T.361, R.366, L.406, I.415, R.418, G.419, Q.422 Ligand excluded by PLIP GOL.22: 8 residues within 4Å: Chain C: R.467, D.607, P.619, V.620, L.621, E.622, Q.625, R.628 Ligand excluded by PLIP GOL.23: 6 residues within 4Å: Chain A: Y.96, L.117 Chain C: Y.152, Q.153, Q.154, Q.172 Ligand excluded by PLIP GOL.24: 5 residues within 4Å: Chain C: Y.573, R.576, A.580, P.613, D.614 Ligand excluded by PLIP GOL.25: 7 residues within 4Å: Chain A: R.100 Chain C: F.351, F.491, D.492, F.523, M.542 Ligands: GOL.19 Ligand excluded by PLIP GOL.26: 9 residues within 4Å: Chain B: R.100 Chain D: N.170, F.351, E.389, E.393, R.441, D.458 Ligands: GOL.17, GOL.28 Ligand excluded by PLIP GOL.27: 7 residues within 4Å: Chain D: T.361, R.366, L.406, I.415, R.418, G.419, Q.422 Ligand excluded by PLIP GOL.28: 12 residues within 4Å: Chain D: L.252, D.280, F.281, W.319, W.386, D.388, E.389, W.455, D.458, F.491, H.521 Ligands: GOL.26 Ligand excluded by PLIP GOL.29: 6 residues within 4Å: Chain B: Y.96, L.117 Chain D: Y.152, Q.153, Q.154, Q.172 Ligand excluded by PLIP GOL.30: 8 residues within 4Å: Chain D: R.467, D.607, P.619, V.620, L.621, E.622, Q.625, R.628 Ligand excluded by PLIP GOL.31: 5 residues within 4Å: Chain D: Y.96, H.119, R.137, V.202, T.204 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matsuzawa, T. et al., Structural insight into substrate specificity of alpha-xylosidase from a soil metagenome. To Be Published

Release Date

2019-04-10

Peptides

Alpha-xylosidase MeXyl31: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
G

Alpha-xylosidase MeXyl31

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