Research workbench
Crystal structure of the holo retinal-bound domain-swapped dimer Q108K:T51D:A28C mutant of human Cellular Retinol Binding Protein II
Analyse Crystal structure of the holo retinal-bound domain-swapped dimer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E7M
- Type
- protein
- Length
- 532 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Homo sapiens
- Molecule
- Retinol-binding protein 2
- UniProt
- P50120
- Ligands
- RET
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · resolution 2.7 · 1 distinct chain · 11% helix, 60% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Retinol-binding protein 2 | protein | 133 | 11% helix, 60% strand | P50120 |
Ligands and binding sites
- RET · Retinal · ligand · chains B, D
- ACT · Acetate ion · additive · 10 copies · chains A, D, C, B
- GOL · Glycerol · additive · 6 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 221 | 0.83 | 0.96 | 34 | empty |
| 2 | 261 | 0.83 | 0.94 | 35 | ACT, RET |
| 3 | 240 | 0.81 | 0.94 | 44 | ACT |
| 4 | 124 | 0.79 | 0.97 | 30 | ACT, GOL |
| 5 | 141 | 0.54 | 0.82 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–C · 4124 Ų buried · 83 hydrogen bonds · protein-protein
- B–D · 3978 Ų buried · 74 hydrogen bonds · protein-protein
- A–D · 515 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 141 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 84 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 cofactor (disulfide, retinal Schiff base).
Compared structures
- 6E7M · Crystal structure of the holo retinal-bound domain-swapped dimer Q108K:T51D:A28C mutant… · the same entry in another collection · chain A against A, TM-score 1.00
- P50120 · AlphaFold monomer V2.0 prediction for retinol-binding protein 2 (P50120) · a predicted model of the same protein · chain A against A, TM-score 0.58
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 6E7M · PDBe 6E7M · UniProt P50120
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