Research workbench
Crystal structure of the holo retinal-bound domain-swapped dimer Q108K:T51D:A28H 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
- 6MCU
- 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 · 1 distinct chain · 11% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Retinol-binding protein 2 | protein | 133 | 11% helix, 57% strand | P50120 |
Ligands and binding sites
- RET · Retinal · ligand · 5 copies · chains F, G, E, H, J, K
- GOL · Glycerol · additive · 3 copies · chains E, F, H, G, 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 251 | 0.84 | 0.96 | 30 | RET |
| 2 | 279 | 0.84 | 0.95 | 38 | empty |
| 3 | 265 | 0.84 | 0.95 | 36 | RET |
| 4 | 234 | 0.84 | 0.96 | 31 | empty |
| 5 | 277 | 0.84 | 0.95 | 38 | empty |
Interfaces
24 interfaces between chains.
- F–G · 4003 Ų buried · 71 hydrogen bonds · protein-protein
- J–K · 3982 Ų buried · 70 hydrogen bonds · protein-protein
- I–L · 3971 Ų buried · 65 hydrogen bonds · protein-protein
- A–D · 3961 Ų buried · 79 hydrogen bonds · protein-protein
- E–H · 3918 Ų buried · 65 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 cofactor (retinal Schiff base).
Compared structures
- 6MCU · Crystal structure of the holo retinal-bound domain-swapped dimer Q108K:T51D:A28H mutant… · 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 6MCU · PDBe 6MCU · UniProt P50120
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