SMTL ID : 6p2l.1

Crystal structure of Niastella koreensis GH74 (NkGH74) enzyme

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.08 Å

Oligo State

monomer

Ligands

1 x GLC- BGC- BGC- BGC- XYS- XYS- XYS- GAL: alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose

GLC-BGC-BGC-BGC-XYS-XYS-XYS-GAL.1: 20 residues within 4Å: Chain A: G.17, F.18, D.36, V.37, Y.88, F.89, H.118, N.120, R.121, L.122, R.124, P.248, S.249, W.347, E.391, V.393, D.411, N.658 Ligands: BGC-BGC-BGC-BGC-XYS-XYS-XYS.2, BGC-BGC-BGC-BGC-XYS-XYS-XYS.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.88, A:N.120, A:R.124, A:R.124, A:F.18, A:D.36, A:D.36, A:N.120, A:R.124, A:R.124, A:D.411, A:H.118, A:N.120 Water bridges: A:Y.88, A:E.391, A:E.391, A:D.411, A:D.411, A:D.411, A:L.122

1 x BGC- BGC- BGC- BGC- XYS- XYS- XYS: alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose

BGC-BGC-BGC-BGC-XYS-XYS-XYS.2: 16 residues within 4Å: Chain A: G.17, F.18, W.299, S.300, W.308, R.343, H.346, W.347, G.366, D.411, Q.412, F.413, T.433 Ligands: GLC-BGC-BGC-BGC-XYS-XYS-XYS-GAL.1, GLC-BGC-BGC-BGC-XYS-XYS-XYS-GAL.1, CL.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.366, A:G.366, A:D.411 Water bridges: A:D.411, A:N.297, A:N.297

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

CL.3: 4 residues within 4Å: Chain A: R.635, S.686, D.687, L.688 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: T.169, S.170, R.199 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: R.567, G.608, I.609, M.663 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: H.25, K.26, P.74 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: W.163, T.214, F.215 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: S.418, N.419, V.420, R.671 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain A: W.43, A.45, S.48, R.360, R.362 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain A: S.538, G.539, N.557, G.559, Q.560 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain A: N.443, A.483, D.484, T.528 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: Q.75, N.76, A.77 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain A: L.161, N.164, T.167 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain A: N.272, N.274, F.313 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain A: T.323, Q.324 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain A: R.343, G.344, H.346, N.367 Ligands: BGC-BGC-BGC-BGC-XYS-XYS-XYS.2 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain A: N.443, N.444, V.445 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain A: K.530, E.573, G.574, N.591 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain A: Q.75, N.135, N.136, S.137 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain A: F.276, A.298, W.299, S.300 Ligand excluded by PLIP CL.21: 5 residues within 4Å: Chain A: P.271, N.272, N.320, T.321, W.322 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain A: S.232, S.233, D.234, T.288 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain A: W.339, K.426, V.427, T.429 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain A: Y.457, T.466, N.504 Ligand excluded by PLIP CL.25: 6 residues within 4Å: Chain A: V.516, Q.517, S.535, P.536, T.537, S.538 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain A: R.645, D.648, D.649 Ligand excluded by PLIP CL.27: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.28: 4 residues within 4Å: Chain A: W.56, S.58, D.649, E.652 Ligand excluded by PLIP CL.29: 5 residues within 4Å: Chain A: Y.194, K.207, L.259, T.261, G.264 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arnal, G. et al., Substrate specificity, regiospecificity, and processivity in glycoside hydrolase family 74. J.Biol.Chem. (2019)

Release Date

2019-07-31

Peptides

Glycosyl hydrolase BNR repeat-containing protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glycosyl hydrolase BNR repeat-containing protein