MolNFT v1 · #19120 · protein
The structure of human retinol binding protein with its carrier protein transthyretin reveals interaction with the carboxy terminus of rbp
1QAB · Protein (transthyretin): “The structure of human retinol binding protein with its carrier protein transthyretin reveals interaction…”. X-ray diffraction, 1 ligand (RTL), 12 pockets (best druggability 0.78). MolNFT v1 #19120 on…
- PDB
- 1QAB
- Type
- protein
- Length
- 820 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (transthyretin); Protein (retinol binding protein)
- UniProt
- P02766, P02753
- Ligands
- RTL
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 5% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (transthyretin) | protein | 124 | 6% helix, 44% strand | P02766 |
| B | Protein (transthyretin) | protein | 118 | 4% helix, 42% strand | P02766 |
| C | Protein (transthyretin) | protein | 114 | 4% helix, 39% strand | P02766 |
| D | Protein (transthyretin) | protein | 113 | 4% helix, 38% strand | P02766 |
| E | Protein (retinol binding protein) | protein | 180 | 4% helix, 14% strand | P02753 |
| F | Protein (retinol binding protein) | protein | 171 | 7% helix, 29% strand | P02753 |
Ligands and binding sites
- RTL · Retinol · ligand · 2 copies · chains D, E, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 357 | 0.78 | 0.87 | 49 | RTL |
| 2 | 342 | 0.76 | 0.87 | 51 | RTL |
| 3 | 454 | 0.76 | 0.85 | 62 | empty |
| 4 | 226 | 0.72 | 0.88 | 32 | empty |
| 5 | 207 | 0.67 | 0.85 | 36 | empty |
Interfaces
12 interfaces between chains.
- A–B · 953 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 935 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 427 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 378 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 375 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 1QAB · The structure of human retinol binding protein with its carrier protein transthyretin… · the same entry in another collection · chain F against F, TM-score 1.00
- P02753 · AlphaFold monomer V2.0 prediction for retinol-binding protein 4 (P02753) · a predicted model of the same protein · chain F against A, TM-score 0.97
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 P02766
- Every structure of UniProt P02753
- Elsewhere: RCSB PDB 1QAB · PDBe 1QAB · UniProt P02766 · UniProt P02753
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