SMTL ID : 8p9u.1

Crystal Structure of Two-Domain Laccase mutant M199A/D268N from Streptomyces griseoflavus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-5-1-mer

Ligands

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

CU.1: 4 residues within 4Å: Chain A: H.193, C.250, H.255, M.260 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.193, A:C.250, A:H.255 CU.2: 5 residues within 4Å: Chain A: H.196, H.198, H.249 Chain C: H.119 Ligands: OXY.4 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Metal complexes: A:H.198, A:H.249, C:H.119 CU.3: 6 residues within 4Å: Chain A: H.64, H.66, H.118 Chain B: H.196, H.251 Ligands: OXY.8 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.66, A:H.118, B:H.251 CU.5: 4 residues within 4Å: Chain B: H.193, C.250, H.255, M.260 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.193, B:C.250, B:H.255 CU.6: 5 residues within 4Å: Chain A: H.120 Chain B: H.196, H.198, H.249 Ligands: OXY.8 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Metal complexes: B:H.198, B:H.249, A:H.120 CU.7: 5 residues within 4Å: Chain B: H.64, H.66, H.118 Chain C: H.250 Ligands: OXY.14 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Metal complexes: C:H.250, B:H.66, B:H.118 CU.10: 4 residues within 4Å: Chain C: H.192, C.249, H.254, M.259 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.192, C:C.249, C:H.254 CU.11: 7 residues within 4Å: Chain A: H.196, H.251 Chain C: H.63, H.65, H.117 Ligands: OXY.4, CU.13 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Metal complexes: C:H.65, C:H.117, A:H.251 CU.12: 4 residues within 4Å: Chain B: H.120 Chain C: H.197, H.248 Ligands: OXY.14 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Metal complexes: C:H.197, C:H.248, B:H.120 CU.13: 6 residues within 4Å: Chain A: H.196 Chain C: H.63, V.64, H.65 Ligands: OXY.4, CU.11 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: C:H.63, A:H.196, H2O.12 CU.15: 4 residues within 4Å: Chain D: H.193, C.250, H.255, M.260 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.193, D:C.250, D:H.255 CU.16: 5 residues within 4Å: Chain D: H.198, M.247, H.249 Chain F: H.120 Ligands: OXY.18 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain F Metal complexes: D:H.198, D:H.249, F:H.120 CU.17: 6 residues within 4Å: Chain D: H.64, H.66, H.118 Chain E: H.196, H.251 Ligands: CU.20 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain D Metal complexes: E:H.251, D:H.66, D:H.118 CU.19: 4 residues within 4Å: Chain E: H.193, C.250, H.255, M.260 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.193, E:C.250, E:H.255 CU.20: 5 residues within 4Å: Chain D: H.120 Chain E: H.196, H.198, H.249 Ligands: CU.17 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain E Metal complexes: D:H.120, E:H.198, E:H.249 CU.21: 5 residues within 4Å: Chain E: H.64, H.66, H.118 Chain F: H.251 Ligands: OXY.26 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain E Metal complexes: F:H.251, E:H.66, E:H.118 CU.22: 5 residues within 4Å: Chain F: H.193, C.250, V.252, H.255, M.260 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.193, F:C.250, F:H.255 CU.23: 6 residues within 4Å: Chain D: H.251 Chain F: H.64, H.66, H.118 Ligands: OXY.18, CU.25 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain D Metal complexes: F:H.66, F:H.118, D:H.251 CU.24: 5 residues within 4Å: Chain E: H.120 Chain F: H.196, H.198, H.249 Ligands: OXY.26 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E Metal complexes: F:H.198, F:H.249, E:H.120 CU.25: 6 residues within 4Å: Chain D: H.196, H.198 Chain F: H.64, H.66 Ligands: OXY.18, CU.23 3 PLIP interactions: 1 interactions with chain F, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: F:H.64, D:H.196, H2O.25

5 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.4: 10 residues within 4Å: Chain A: H.196, H.198, H.249, H.251 Chain C: H.63, H.117, H.119 Ligands: CU.2, CU.11, CU.13 No protein-ligand interaction detected (PLIP) OXY.8: 9 residues within 4Å: Chain A: H.64, H.118, H.120 Chain B: H.196, H.198, H.249, H.251 Ligands: CU.3, CU.6 No protein-ligand interaction detected (PLIP) OXY.14: 8 residues within 4Å: Chain B: H.64, H.120 Chain C: H.195, H.197, H.248, H.250 Ligands: CU.7, CU.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.64 OXY.18: 10 residues within 4Å: Chain D: H.196, H.198, H.249, H.251 Chain F: H.64, H.118, H.120 Ligands: CU.16, CU.23, CU.25 No protein-ligand interaction detected (PLIP) OXY.26: 9 residues within 4Å: Chain E: H.64, H.118, H.120 Chain F: H.196, H.198, H.249, H.251 Ligands: CU.21, CU.24 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-functional Binders)

CA.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.27: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kolyadenko, I. et al., Structural Insight into the Amino Acid Environment of the Two-Domain Laccase's Trinuclear Copper Cluster. Int J Mol Sci (2023)

Release Date

2024-04-10

Peptides

Two-domain laccase: ABDEF
Two-domain laccase: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
D

E
E

F
F

C
C

Two-domain laccase

Two-domain laccase