MolNFT v1 · #127030 · protein
Crystal structure of two-domain laccase mutant H165F from streptomyces griseoflavus
5MKM: “Crystal structure of two-domain laccase mutant H165F from streptomyces griseoflavus”. X-ray diffraction, 4 ligands (CU, OXY, O), 16 pockets (best druggability 0.88). MolNFT v1 #127030 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5MKM
- Type
- protein
- Length
- 1,660 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, OXY, O, SO4
- Pockets
- 16 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Two-domain laccase (EC 1.10.3.2) | protein | 278 | 6% helix, 42% strand | A0A0M4FJ81 |
| C, F | Two-domain laccase (EC 1.10.3.2) | protein | 275 | 5% helix, 42% strand | A0A0M4FJ81 |
| D, E | Two-domain laccase (EC 1.10.3.2) | protein | 277 | 7% helix, 42% strand | A0A0M4FJ81 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 12 copies · chains A, B, C, D, E, F
- OXY · Oxygen molecule · ion · 2 copies · chains A, B, D, E
- O · Oxygen atom · ion · 2 copies · chains A, C, D, F
- SO4 · Sulfate ion · ion · chains F
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, C, E, F
- GOL · Glycerol · additive · chains D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 913 | 0.88 | 0.89 | 104 | empty |
| 2 | 418 | 0.86 | 0.94 | 66 | EDO |
| 3 | 631 | 0.85 | 0.89 | 96 | GOL, EDO |
| 4 | 291 | 0.76 | 0.88 | 52 | empty |
| 5 | 67 | 0.71 | 0.97 | 19 | empty |
Interfaces
13 interfaces between chains.
- D–F · 1799 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 1794 Ų buried · 37 hydrogen bonds · protein-protein
- D–E · 1776 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 1773 Ų buried · 31 hydrogen bonds · protein-protein
- E–F · 1759 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 5MKM · Crystal Structure of Two-Domain Laccase mutant H165F from Streptomyces griseoflavus · the same entry in another collection · chain E against E, 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 5MKM · PDBe 5MKM · UniProt A0A0M4FJ81
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