SMTL ID : 5o4i.3 (3 other biounits)

Crystal Structure of mutant M54L/M64L/M96L of Two-Domain Laccase from Streptomyces griseoflavus dialyzed against solution containing 0.25 mM copper sulfate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-trimer

Ligands

9 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.235, H.237, H.288 Chain C: H.103, H.159 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: A:H.237, A:H.288, C:H.159, H2O.3 CU.3: 6 residues within 4Å: Chain A: H.103, H.105, H.157 Chain B: H.235, H.290 Ligands: CU.11 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:H.105, A:H.157, B:H.290, H2O.5 CU.10: 5 residues within 4Å: Chain B: H.232, C.289, V.291, 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: 6 residues within 4Å: Chain A: H.103, H.159 Chain B: H.235, H.237, H.288 Ligands: CU.3 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:H.237, B:H.288, A:H.159, H2O.5 CU.12: 4 residues within 4Å: Chain B: H.103, H.105, H.157 Chain C: H.290 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:H.103, B:H.105, B:H.157, C:H.290, H2O.7 CU.15: 4 residues within 4Å: Chain A: H.290 Chain C: H.103, H.105, H.157 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: C:H.103, C:H.105, C:H.157, A:H.290, H2O.3 CU.16: 4 residues within 4Å: Chain C: 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.17: 5 residues within 4Å: Chain B: H.103, H.159 Chain C: H.235, H.237, H.288 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: C:H.237, C:H.288, B:H.159, H2O.7

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: D.243, K.262, D.268 Chain B: Q.257, N.261, K.262, I.263 Ligands: GOL.8 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Q.257, B:Q.257, B:N.261, B:I.263, A:K.262 Water bridges: A:D.243, A:K.262, A:D.268 GOL.5: 9 residues within 4Å: Chain A: G.152, Y.153, W.154, N.244, R.245, S.269 Chain B: Q.257, V.258, I.259 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Y.153, A:Y.153, B:Q.257 Water bridges: A:S.269, A:S.269, B:Q.257, B:D.260 GOL.6: 7 residues within 4Å: Chain A: Q.257, N.261, K.262, I.263 Chain C: K.262, D.268 Ligands: GOL.8 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:Q.257, A:Q.257, A:N.261, A:I.263, C:K.262 Water bridges: C:D.243 GOL.7: 6 residues within 4Å: Chain A: D.243, Q.257 Chain B: D.243, Q.257 Chain C: D.243, Q.257 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 3 interactions with chain B Hydrogen bonds: A:Q.257, C:Q.257, B:D.243, B:D.243, B:Q.257 GOL.8: 9 residues within 4Å: Chain A: K.262, I.263 Chain B: D.243, K.262 Chain C: K.262, I.263 Ligands: GOL.4, GOL.6, GOL.13 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.262 GOL.13: 7 residues within 4Å: Chain B: K.262, D.268 Chain C: Q.257, N.261, K.262, I.263 Ligands: GOL.8 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:Q.257, C:Q.257, C:N.261, C:I.263, B:K.262, B:K.262 GOL.14: 8 residues within 4Å: Chain B: G.152, Y.153, W.154, R.245, S.269 Chain C: Q.257, V.258, I.259 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:Q.257, B:Y.153, B:S.269 Water bridges: B:S.269, B:S.269 GOL.18: 9 residues within 4Å: Chain A: Q.257, V.258, I.259 Chain C: G.152, Y.153, W.154, N.244, R.245, S.269 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:Q.257, C:Y.153 Water bridges: A:D.260, C:S.269, C:S.269 GOL.19: 5 residues within 4Å: Chain C: K.117, V.160, G.162, T.163, E.164 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.162, C:T.163 GOL.20: 5 residues within 4Å: Chain C: E.137, P.138, G.139, R.140, R.147 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.137, C:R.147 Water bridges: C:E.137

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

SO4.9: 4 residues within 4Å: Chain A: R.182, R.245 Chain B: D.254, P.255 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Water bridges: A:R.182 Salt bridges: A:R.182, A:R.245 Hydrogen bonds: B:P.255

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gabdulkhakov, A.G. et al., Incorporation of Copper Ions into T2/T3 Centers of Two-Domain Laccases. Mol.Biol.(Moscow) (2018)

Release Date

2018-03-28

Peptides

Two-domain laccase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
I

Two-domain laccase

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