MolNFT v1 · #127586 · protein
HPAD4 crystal complex with afm-41A
5N0Z · Protein-arginine deiminase type-4: “HPAD4 crystal complex with afm-41A”. X-ray diffraction, 3 ligands (8FT, CA, SO4), 4 pockets (best druggability 0.53). MolNFT v1 #127586 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5N0Z
- Type
- protein
- Length
- 638 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein-arginine deiminase type-4
- EC
- 3.5.3.15
- UniProt
- Q9UM07
- Ligands
- 8FT, CA, SO4
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein-arginine deiminase type-4 (EC 3.5.3.15) | protein | 638 | 21% helix, 37% strand | Q9UM07 |
Ligands and binding sites
- 8FT · 2-ethyl-~{N}-[(1~{S})-4-(2-fluoranylethanimidoylamino)-1-(4-methoxy-1-methyl-benzimidazol-2-yl)butyl]-3-oxidanylidene-1~{H}-isoindole-4-carboxamide · ligand · chains A
- CA · Calcium ion · metal · 5 copies · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.53 | 0.87 | 23 | empty |
| 2 | 123 | 0.42 | 0.76 | 19 | SO4, 8FT |
| 3 | 104 | 0.40 | 0.76 | 30 | empty |
| 4 | 74 | 0.35 | 0.76 | 18 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
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 Q9UM07
- Elsewhere: RCSB PDB 5N0Z · PDBe 5N0Z · UniProt Q9UM07
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