MolNFT v1 · #159838 · protein
Crystal structure of AFV00434, an ancestral GH74 enzyme
6P2K · Fibronectin type III domain-containing protein: “Crystal structure of AFV00434, an ancestral GH74 enzyme”. X-ray diffraction, 2 ligands (ZN, CL), 10 pockets (best druggability 0.82). MolNFT v1 #159838 on GenesisL1: 3D structure…
- PDB
- 6P2K
- Type
- protein
- Length
- 1,554 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fibronectin type III domain-containing protein
- UniProt
- K4KQN2
- Ligands
- ZN, CL
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fibronectin type III domain-containing protein | protein | 776 | 4% helix, 50% strand | K4KQN2 |
| B | Fibronectin type III domain-containing protein | protein | 778 | 4% helix, 49% strand | K4KQN2 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 14 copies · chains A, B
- PE3 · 3,6,9,12,15,18,21,24,27,30,33,36,39-tridecaoxahentetracontane-1,41-diol · additive · 6 copies · chains A, B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 727 | 0.82 | 0.86 | 56 | empty |
| 2 | 807 | 0.82 | 0.85 | 72 | GOL |
| 3 | 532 | 0.71 | 0.80 | 48 | ZN |
| 4 | 567 | 0.70 | 0.79 | 48 | ZN, PE3 |
| 5 | 258 | 0.69 | 0.84 | 49 | empty |
Interfaces
1 interface between chains.
- A–B · 312 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6P2K · Crystal structure of AFV00434, an ancestral GH74 enzyme · the same entry in another collection · chain A against A, 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 K4KQN2
- Elsewhere: RCSB PDB 6P2K · PDBe 6P2K · UniProt K4KQN2
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