SMTL ID : 6zps.1

Structure of Unliganded MgGH51 a-L-Arabinofuranosidase Crystal Type 3 Collected at 2.75 A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN.1: 8 residues within 4Å: Chain A: W.386, N.387, V.389, V.393, Q.419, N.421, T.423 Ligands: ACT.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.387

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 6 residues within 4Å: Chain A: W.102, V.486, N.487, D.499, P.591, E.592 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.591 Hydrogen bonds: A:E.592 NAG-NAG.4: 8 residues within 4Å: Chain A: Q.144, N.145, N.160, L.161, E.162, L.163, H.164 Ligands: CL.37 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.3: 10 residues within 4Å: Chain A: R.241, Q.243, N.245, A.246, D.253, P.255, P.307, Y.308, Q.311 Ligands: CL.22 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.307, A:Y.308 Hydrogen bonds: A:R.241 Water bridges: A:R.241, A:Y.308

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 10 residues within 4Å: Chain A: M.21, E.23, I.25, N.231, W.261, Y.402, E.429, A.480, P.481, W.491 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.402, A:E.429 Water bridges: A:E.23, A:N.231, A:N.231, A:N.231

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 6 residues within 4Å: Chain A: W.386, F.418, Q.419, Y.425 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.418 Hydrogen bonds: A:Q.419 Water bridges: A:Q.419 ACT.20: 3 residues within 4Å: Chain A: N.204, R.205, P.206 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.205

13 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 3 residues within 4Å: Chain A: S.573, S.574, T.575 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.574, A:S.574 SO4.8: 1 residues within 4Å: Chain A: R.150 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.150, A:R.150 Salt bridges: A:R.150 SO4.9: 3 residues within 4Å: Chain A: P.584, E.585, F.617 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.585 Water bridges: A:E.585 SO4.10: 1 residues within 4Å: Chain A: R.205 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.205 SO4.11: 5 residues within 4Å: Chain A: T.530, G.533, T.534, L.535, Q.560 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.530, A:T.534, A:T.534, A:L.535, A:Q.560 SO4.12: 2 residues within 4Å: Chain A: T.4, T.527 3 PLIP interactions: 3 interactions with chain A Water bridges: A:T.4, A:T.527, A:L.528 SO4.13: 6 residues within 4Å: Chain A: V.13, P.14, S.15, K.519, G.520, D.521 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.519 Water bridges: A:K.519, A:K.519, A:K.519, A:K.519, A:D.521, A:D.521 Salt bridges: A:K.519 SO4.14: 1 residues within 4Å: Chain A: S.125 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.125 Water bridges: A:S.125, A:S.125 SO4.15: 2 residues within 4Å: Chain A: H.58, P.59 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.58 SO4.16: 3 residues within 4Å: Chain A: S.146, T.147, Q.148 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.148 Water bridges: A:S.146 SO4.17: 2 residues within 4Å: Chain A: G.139, R.140 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.139 Salt bridges: A:R.140 SO4.18: 5 residues within 4Å: Chain A: T.237, T.238, S.294, T.298, L.300 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.238, A:T.238, A:T.238, A:T.298 Water bridges: A:A.239 SO4.19: 4 residues within 4Å: Chain A: P.14, S.15, T.16, R.344 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.15, A:T.16 Water bridges: A:T.16 Salt bridges: A:R.344

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

CL.21: 3 residues within 4Å: Chain A: S.326, A.327, P.328 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain A: Q.243 Ligands: NAG-NAG-BMA-MAN-MAN.3 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain A: T.50, A.51 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain A: I.60, S.61 Ligand excluded by PLIP CL.25: 5 residues within 4Å: Chain A: T.404, P.405, T.406, T.435, Q.455 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain A: P.87, S.88 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain A: V.1, T.2 Ligand excluded by PLIP CL.28: 2 residues within 4Å: Chain A: S.558, A.559 Ligand excluded by PLIP CL.29: 2 residues within 4Å: Chain A: P.9, Q.522 Ligand excluded by PLIP CL.30: 3 residues within 4Å: Chain A: Q.144, N.145, S.146 Ligand excluded by PLIP CL.31: 2 residues within 4Å: Chain A: N.62, P.87 Ligand excluded by PLIP CL.32: 2 residues within 4Å: Chain A: N.6, N.8 Ligand excluded by PLIP CL.33: 1 residues within 4Å: Chain A: T.443 Ligand excluded by PLIP CL.34: 3 residues within 4Å: Chain A: T.534, G.556, S.557 Ligand excluded by PLIP CL.35: 1 residues within 4Å: Chain A: K.608 Ligand excluded by PLIP CL.36: 2 residues within 4Å: Chain A: A.55, A.56 Ligand excluded by PLIP CL.37: 1 residues within 4Å: Ligands: NAG-NAG.4 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McGregor, N.G.S. et al., Structure of a GH51 alpha-L-arabinofuranosidase from Meripilus giganteus: conserved substrate recognition from bacteria to fungi. Acta Crystallogr D Struct Biol (2020)

Release Date

2020-11-11

Peptides

MgGH51: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

MgGH51

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