MolNFT v1 · #125726 · protein

Crystal structure of two-domain laccase from streptomyces griseoflavus

5LHL: “Crystal structure of two-domain laccase from streptomyces griseoflavus”. X-ray diffraction, 4 ligands (CU, NA, OXY), 18 pockets (best druggability 0.88). MolNFT v1 #125726 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5LHL
Type: protein
Length: 1,659 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Two-domain laccase
EC: 1.10.3.2
UniProt: A0A0M4FJ81
Ligands: CU, NA, OXY, CL
Pockets: 18 · best druggability 0.88

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Two-domain laccase (EC 1.10.3.2)	protein	278	5% helix, 43% strand	A0A0M4FJ81
C, E, F	Two-domain laccase (EC 1.10.3.2)	protein	275	7% helix, 42% strand	A0A0M4FJ81

Ligands and binding sites

CU · Copper (II) ion · metal · 24 copies · chains A, C, B, D, F, E
NA · Sodium ion · metal · 2 copies · chains A, B, C, D, E, F
OXY · Oxygen molecule · ion · 6 copies · chains A, B, C, D, F, E
CL · Chloride ion · ion · 3 copies · chains A, B, E

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

18 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	969	0.88	0.90	105	empty
2	427	0.84	0.92	66	NA
3	573	0.82	0.88	86	NA
4	371	0.77	0.87	44	empty
5	62	0.72	0.98	19	empty

Interfaces

14 interfaces between chains.

A–C · 1778 Å² buried · 34 hydrogen bonds · protein-protein
D–F · 1756 Å² buried · 36 hydrogen bonds · protein-protein
B–C · 1746 Å² buried · 32 hydrogen bonds · protein-protein
A–B · 1746 Å² buried · 35 hydrogen bonds · protein-protein
E–F · 1710 Å² buried · 27 hydrogen bonds · protein-protein

Compared structures

5LHL · Crystal Structure of Two-Domain Laccase from Streptomyces griseoflavus · the same entry in another collection · chain F against F, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt A0A0M4FJ81
Elsewhere: RCSB PDB 5LHL · PDBe 5LHL · UniProt A0A0M4FJ81

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