Research workbench
Crystal structure of the human retinal protein 4 (unc-119 homolog a). northeast structural genomics consortium target HR3066A
Analyse Crystal structure of the human retinal protein 4 (unc-119 homolog a). northeast… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GQQ
- Type
- protein
- Length
- 1,025 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein unc-119 homolog a
- UniProt
- Q13432
- Ligands
- UNL
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 12% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein unc-119 homolog a | protein | 167 | 12% helix, 47% strand | Q13432 |
| B | Protein unc-119 homolog a | protein | 178 | 12% helix, 42% strand | Q13432 |
| C | Protein unc-119 homolog a | protein | 170 | 12% helix, 44% strand | Q13432 |
| D | Protein unc-119 homolog a | protein | 181 | 11% helix, 43% strand | Q13432 |
| E | Protein unc-119 homolog a | protein | 165 | 12% helix, 47% strand | Q13432 |
| F | Protein unc-119 homolog a | protein | 164 | 11% helix, 46% strand | Q13432 |
Ligands and binding sites
- UNL · Unknown ligand · ion · 30 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 394 | 0.80 | 0.88 | 56 | UNL |
| 2 | 572 | 0.80 | 0.85 | 60 | UNL |
| 3 | 446 | 0.79 | 0.87 | 53 | UNL |
| 4 | 415 | 0.79 | 0.87 | 54 | UNL |
| 5 | 388 | 0.79 | 0.88 | 59 | UNL |
Interfaces
9 interfaces between chains.
- A–D · 823 Ų buried · 15 hydrogen bonds · protein-protein
- C–E · 632 Ų buried · 6 hydrogen bonds · protein-protein
- C–F · 544 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 408 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 375 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 3GQQ · Crystal structure of the human retinal protein 4 (unc-119 homolog A). Northeast… · the same entry in another collection · chain F against F, TM-score 1.00
- Q13432 · AlphaFold monomer V2.0 prediction for protein unc-119 homolog a (Q13432) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q13432
- Elsewhere: RCSB PDB 3GQQ · PDBe 3GQQ · UniProt Q13432
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