SMTL ID : 5nq9.1

Crystal structure of laccases from Pycnoporus sanguineus, izoform II, monoclinic

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.72 Å

Oligo State

homo-dimer

Ligands

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

NAG-NAG-MAN-MAN-MAN.1: 2 residues within 4Å: Chain A: N.361, N.362 No protein-ligand interaction detected (PLIP)

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: P.346, L.347, N.348, S.404, P.406, N.455 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.346 Hydrogen bonds: A:N.348 NAG-NAG.4: 4 residues within 4Å: Chain B: N.348, S.404, P.406, N.455 2 PLIP interactions: 2 interactions with chain B Water bridges: B:P.346, B:N.348

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

NAG-NAG-BMA.3: 9 residues within 4Å: Chain A: R.43, E.44, N.75, T.77, M.78, H.174, V.175, A.176, L.179 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.43 Hydrogen bonds: A:A.176 NAG-NAG-BMA.5: 9 residues within 4Å: Chain B: R.43, E.44, N.75, T.77, M.78, H.174, V.175, A.176, L.179 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.43, B:A.176 Hydrogen bonds: B:A.176

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

CU.6: 5 residues within 4Å: Chain A: H.416, C.472, I.474, H.477, F.482 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.416, A:C.472, A:H.477 CU.7: 5 residues within 4Å: Chain A: H.85, H.87, H.419, H.421 Ligands: PER.10 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.85, A:H.419, H2O.2 CU.8: 6 residues within 4Å: Chain A: H.85, H.87, W.128, H.130, H.473 Ligands: PER.10 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.87, A:H.130, A:H.473 CU.9: 5 residues within 4Å: Chain A: H.132, H.419, H.421, H.471 Ligands: PER.10 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.132, A:H.421, A:H.471 CU.22: 1 residues within 4Å: Chain A: E.44 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.44 CU.23: 1 residues within 4Å: Chain A: D.205 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.205 CU.25: 5 residues within 4Å: Chain B: H.416, C.472, I.474, H.477, F.482 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.416, B:C.472, B:H.477 CU.26: 5 residues within 4Å: Chain B: H.85, H.87, H.419, H.421 Ligands: PER.24 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.85, B:H.419 CU.27: 5 residues within 4Å: Chain B: H.132, H.419, H.421, H.471 Ligands: PER.24 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.132, B:H.421, B:H.471 CU.28: 6 residues within 4Å: Chain B: H.85, H.87, W.128, H.130, H.473 Ligands: PER.24 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.87, B:H.130, B:H.473 CU.37: 1 residues within 4Å: Chain B: E.44 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.44, H2O.3 CU.38: 1 residues within 4Å: Chain B: D.205 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.205

2 x PER: PEROXIDE ION(Non-covalent)

PER.10: 11 residues within 4Å: Chain A: H.85, H.87, H.130, H.132, H.419, H.421, H.471, H.473 Ligands: CU.7, CU.8, CU.9 No protein-ligand interaction detected (PLIP) PER.24: 11 residues within 4Å: Chain B: H.85, H.87, H.130, H.132, H.419, H.421, H.471, H.473 Ligands: CU.26, CU.27, CU.28 No protein-ligand interaction detected (PLIP)

7 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.11: 5 residues within 4Å: Chain A: P.25, G.62, D.63, R.64 Ligands: PEG.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.64, A:R.64 PEG.12: 4 residues within 4Å: Chain A: V.26, R.64, Q.66 Ligands: PEG.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.66 PEG.13: 5 residues within 4Å: Chain A: V.26, A.27, D.28, Q.66, N.68 No protein-ligand interaction detected (PLIP) PEG.14: 5 residues within 4Å: Chain A: T.231, N.283, P.284, S.285, T.289 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.283, A:T.289 PEG.30: 5 residues within 4Å: Chain A: P.412, G.413, A.414 Chain B: N.354, T.356 No protein-ligand interaction detected (PLIP) PEG.31: 8 residues within 4Å: Chain B: A.101, H.132, L.133, S.134, F.365, P.367, L.478, D.479 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.134, B:D.479 PEG.32: 5 residues within 4Å: Chain B: T.231, N.283, P.284, S.285, T.289 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.283, B:T.289, B:T.289

11 x FMT: FORMIC ACID(Non-functional Binders)

FMT.15: 3 residues within 4Å: Chain A: H.76, T.77, K.178 No protein-ligand interaction detected (PLIP) FMT.16: 1 residues within 4Å: Chain A: D.161 No protein-ligand interaction detected (PLIP) FMT.17: 1 residues within 4Å: Chain A: N.352 No protein-ligand interaction detected (PLIP) FMT.18: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.352 FMT.19: 2 residues within 4Å: Chain A: Q.60 Ligands: FMT.20 No protein-ligand interaction detected (PLIP) FMT.20: 2 residues within 4Å: Chain A: S.58 Ligands: FMT.19 No protein-ligand interaction detected (PLIP) FMT.21: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) FMT.33: 3 residues within 4Å: Chain B: Q.60, Y.148, P.150 No protein-ligand interaction detected (PLIP) FMT.34: 3 residues within 4Å: Chain B: A.155, Y.158, D.159 No protein-ligand interaction detected (PLIP) FMT.35: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) FMT.36: 1 residues within 4Å: Chain B: A.292 No protein-ligand interaction detected (PLIP)

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

NAG.29: 2 residues within 4Å: Chain A: N.354 Chain B: N.362 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.362

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Orlikowska, M. et al., Structural studies of two thermostable laccases from the white-rot fungus Pycnoporus sanguineus. Int. J. Biol. Macromol. (2018)

Release Date

2017-11-01

Peptides

Laccase, izoform II: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Laccase, izoform II

Related Entries With Identical Sequence