MolNFT v1 · #167371 · protein
The crystal structure of domain-swapped trimer Q108K:K40D:T53A:R58L:Q38F:Q4F:V62E variant of hcrbpii
6VIS · Retinol-binding protein 2: “The crystal structure of domain-swapped trimer Q108K:K40D:T53A:R58L:Q38F:Q4F:V62E variant of hcrbpii”. X-ray diffraction, 5 pockets (best druggability 0.83). MolNFT v1 #167371 on GenesisL1: 3D structure…
- PDB
- 6VIS
- Type
- protein
- Length
- 399 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinol-binding protein 2
- UniProt
- P50120
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Retinol-binding protein 2 | protein | 133 | 11% helix, 59% strand | P50120 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 447 | 0.83 | 0.90 | 47 | GOL |
| 2 | 269 | 0.81 | 0.92 | 36 | empty |
| 3 | 400 | 0.79 | 0.88 | 53 | empty |
| 4 | 142 | 0.45 | 0.77 | 24 | empty |
| 5 | 60 | 0.31 | 0.75 | 15 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2076 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 2059 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 1998 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 6VIS · The Crystal Structure of Domain-Swapped Trimer Q108K:K40D:T53A:R58L:Q38F:Q4F:V62E Variant… · 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 P50120
- Elsewhere: RCSB PDB 6VIS · PDBe 6VIS · UniProt P50120
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