SMTL ID : 5nkw.1

X-ray crystal structure of an AA9 LPMO

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

monomer

Ligands

1 x BMA- BGC- BMA- BGC- BGC- BMA- BGC: beta-D-glucopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-mannopyranose

BMA-BGC-BMA-BGC-BGC-BMA-BGC.1: 17 residues within 4Å: Chain A: H.1, N.28, H.66, N.67, A.75, S.77, H.78, H.147, E.148, R.159, Y.203, T.204 Ligands: CU.3, CL.8, CL.10, CL.20, BGC.22 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.164, A:Y.164

1 x BMA- BMA- BGC: beta-D-glucopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose

BMA-BMA-BGC.2: 10 residues within 4Å: Chain A: V.9, V.12, D.13, Q.14, P.53, V.54, N.55, D.58, N.173 Ligands: BMA.23 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.55, A:D.58, A:N.173, A:Q.14 Water bridges: A:N.10, A:N.55, A:S.174, A:Q.14

1 x CU: COPPER (II) ION(Non-covalent)

CU.3: 6 residues within 4Å: Chain A: H.1, H.78, Q.162, Y.164 Ligands: BMA-BGC-BMA-BGC-BGC-BMA-BGC.1, CL.8 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.78, A:Y.164, H2O.9

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

NAG.4: 5 residues within 4Å: Chain A: N.33, T.35, S.36, P.37, Y.153 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.33, A:T.35, A:Y.153 Water bridges: A:S.36

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

CL.5: 4 residues within 4Å: Chain A: T.120, A.121, A.227, Q.228 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: N.27, N.29 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: T.35, G.189 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain A: H.1, H.147, Q.162 Ligands: BMA-BGC-BMA-BGC-BGC-BMA-BGC.1, CU.3 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: V.211, A.212 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: H.66 Ligands: BMA-BGC-BMA-BGC-BGC-BMA-BGC.1 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: T.59 Ligands: CL.14 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain A: K.50, S.51 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain A: V.31, K.32, N.33 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain A: S.126, G.224, S.225 Ligands: CL.11 Ligand excluded by PLIP CL.15: 6 residues within 4Å: Chain A: V.132, A.133, Y.137, D.177, P.180, L.181 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain A: A.89, A.90, D.136 Ligands: CL.17 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain A: A.90 Ligands: CL.16 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain A: F.102, E.103 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain A: W.218, S.219 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain A: A.75, S.76, S.77 Ligands: BMA-BGC-BMA-BGC-BGC-BMA-BGC.1 Ligand excluded by PLIP CL.21: 1 residues within 4Å: Chain A: P.157 Ligand excluded by PLIP

1 x BGC: beta-D-glucopyranose(Non-covalent)

BGC.22: 3 residues within 4Å: Chain A: N.67 Ligands: BMA-BGC-BMA-BGC-BGC-BMA-BGC.1, BMA-BGC-BMA-BGC-BGC-BMA-BGC.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.67 Water bridges: A:N.28

1 x BMA: beta-D-mannopyranose(Non-covalent)

BMA.23: 7 residues within 4Å: Chain A: P.53, V.54, N.55, D.58, N.173 Ligands: BMA-BMA-BGC.2, BMA-BMA-BGC.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.55, A:D.58, A:N.173 Water bridges: A:N.55, A:S.174

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Simmons, T.J. et al., Structural and electronic determinants of lytic polysaccharide monooxygenase reactivity on polysaccharide substrates. Nat Commun (2017)

Release Date

2017-11-01

Peptides

Auxiliary activity 9: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Auxiliary activity 9

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