SMTL ID : 6zij.1 (1 other biounit)

Crystal Structure of Two-Domain Laccase mutant R240H from Streptomyces griseoflavus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-trimer

Ligands

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

CU.1: 4 residues within 4Å: Chain A: H.232, C.289, H.294, M.299 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.232, A:C.289, A:H.294 CU.2: 5 residues within 4Å: Chain A: H.237, M.286, H.288 Chain C: H.159 Ligands: OXY.7 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Metal complexes: C:H.159, A:H.237, A:H.288 CU.5: 6 residues within 4Å: Chain A: H.103, H.105, H.157 Chain B: H.290 Ligands: CU.6, OXY.8 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.105, A:H.157, B:H.290 CU.6: 6 residues within 4Å: Chain A: H.103, H.105 Chain B: H.235, H.237 Ligands: CU.5, OXY.8 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:H.235, A:H.103, H2O.1 CU.10: 4 residues within 4Å: Chain B: H.232, C.289, H.294, M.299 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.232, B:C.289, B:H.294 CU.11: 4 residues within 4Å: Chain A: H.159 Chain B: H.237, H.288 Ligands: OXY.8 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Metal complexes: B:H.237, B:H.288, A:H.159 CU.13: 6 residues within 4Å: Chain B: H.103, H.105, H.157 Chain C: H.290 Ligands: OXY.14, CU.19 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Metal complexes: C:H.290, B:H.105, B:H.157 CU.15: 6 residues within 4Å: Chain A: H.290 Chain C: H.103, H.105, H.157 Ligands: OXY.7, CU.16 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Metal complexes: C:H.105, C:H.157, A:H.290 CU.16: 6 residues within 4Å: Chain A: H.235, H.237 Chain C: H.103, H.105 Ligands: OXY.7, CU.15 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Metal complexes: C:H.103, A:H.235 CU.17: 5 residues within 4Å: Chain C: Y.231, H.232, C.289, H.294, M.299 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.232, C:C.289, C:H.294 CU.18: 4 residues within 4Å: Chain B: H.159 Chain C: H.237, H.288 Ligands: OXY.14 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Metal complexes: C:H.237, C:H.288, B:H.159 CU.19: 6 residues within 4Å: Chain B: H.103, H.105 Chain C: H.235, H.237 Ligands: CU.13, OXY.14 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Metal complexes: B:H.103, C:H.235

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: G.152, Y.153, I.179, V.180, R.181, D.185, R.245, T.246 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.152, A:R.181, A:R.245 Water bridges: A:D.185, A:Q.273 GOL.20: 9 residues within 4Å: Chain C: A.151, G.152, Y.153, I.179, V.180, R.181, D.185, R.245, T.246 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:G.152, C:Y.153, C:R.181, C:D.185, C:R.245 Water bridges: C:Y.153, C:D.185, C:V.186

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 5 residues within 4Å: Chain A: R.50, L.79, I.80, E.81, L.82 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.79, A:E.81 EDO.12: 8 residues within 4Å: Chain B: A.151, G.152, Y.153, I.179, V.180, R.181, D.185, R.245 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.152, B:R.181, B:D.185, B:R.245 Water bridges: B:V.186

3 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.7: 11 residues within 4Å: Chain A: H.235, H.237, H.288, H.290 Chain C: H.103, H.105, H.157, H.159 Ligands: CU.2, CU.15, CU.16 No protein-ligand interaction detected (PLIP) OXY.8: 10 residues within 4Å: Chain A: H.103, H.157, H.159 Chain B: H.235, H.237, H.288, H.290 Ligands: CU.5, CU.6, CU.11 No protein-ligand interaction detected (PLIP) OXY.14: 11 residues within 4Å: Chain B: H.103, H.105, H.157, H.159 Chain C: H.235, H.237, H.288, H.290 Ligands: CU.13, CU.18, CU.19 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.21: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gabdulkhakov, A. et al., The role of positive charged residue in the proton-transfer mechanism of two-domain laccase from Streptomyces griseoflavus Ac-993. J.Biomol.Struct.Dyn. (2022)

Release Date

2021-05-05

Peptides

Two-domain laccase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Two-domain laccase

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