MolNFT v1 · #186601 · protein
Crystal structure of the vitronectin hemopexin-like domain binding calcium
7RJ9: “Crystal structure of the vitronectin hemopexin-like domain binding calcium”. X-ray diffraction, 4 ligands (CA, NA, CL), 5 pockets (best druggability 0.76). MolNFT v1 #186601 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7RJ9
- Type
- protein
- Length
- 383 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitronectin
- UniProt
- P04004
- Ligands
- CA, NA, CL, SO4
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitronectin | protein | 189 | 8% helix, 40% strand | P04004 |
| B | Vitronectin | protein | 194 | 9% helix, 39% strand | P04004 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 539 | 0.76 | 0.83 | 69 | SO4 |
| 2 | 110 | 0.45 | 0.78 | 20 | empty |
| 3 | 86 | 0.43 | 0.79 | 22 | empty |
| 4 | 51 | 0.29 | 0.75 | 15 | empty |
| 5 | 57 | 0.28 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 864 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
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 P04004
- Elsewhere: RCSB PDB 7RJ9 · PDBe 7RJ9 · UniProt P04004
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