MolNFT v1 · #135688 · protein
Crystal structure of the holo domain-swapped dimer mutant Q108K:K40D human cellular retinol binding protein II bound with all trans retinal
5U6G · Retinol-binding protein 2: “Crystal structure of the holo domain-swapped dimer mutant Q108K:K40D human cellular retinol binding protein…”. X-ray diffraction, 1 ligand (RET), 20 pockets (best druggability 0.84). MolNFT v1 #135688 on…
- PDB
- 5U6G
- Type
- protein
- Length
- 1,596 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinol-binding protein 2
- UniProt
- P50120
- Ligands
- RET
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 60% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, H, E, F, J, K, L | Retinol-binding protein 2 | protein | 133 | 11% helix, 60% strand | P50120 |
| G, I | Retinol-binding protein 2 | protein | 133 | 11% helix, 60% strand | P50120 |
Ligands and binding sites
- RET · Retinal · ligand · 11 copies · chains A, F, B, E, C, G, D, H, I, K, J, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 272 | 0.84 | 0.95 | 41 | RET |
| 2 | 275 | 0.84 | 0.95 | 38 | RET |
| 3 | 280 | 0.84 | 0.94 | 34 | RET |
| 4 | 272 | 0.83 | 0.94 | 39 | RET |
| 5 | 240 | 0.83 | 0.95 | 36 | RET |
Interfaces
37 interfaces between chains.
- C–G · 3965 Ų buried · 76 hydrogen bonds · protein-protein
- I–K · 3934 Ų buried · 77 hydrogen bonds · protein-protein
- B–E · 3908 Ų buried · 81 hydrogen bonds · protein-protein
- A–F · 3902 Ų buried · 74 hydrogen bonds · protein-protein
- D–H · 3894 Ų buried · 75 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 cofactor (retinal Schiff base).
Compared structures
- 5U6G · Crystal Structure of the holo Domain-Swapped Dimer mutant Q108K:K40D Human Cellular… · the same entry in another collection · chain L against L, 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 5U6G · PDBe 5U6G · UniProt P50120
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