Research workbench
The structure of human retinol binding protein with its carrier protein transthyretin reveals interaction with the carboxy terminus of rbp
Analyse The structure of human retinol binding protein with its carrier protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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