Research workbench
Crystal structure of human RAB11-RABIN8-FIP3
Analyse Crystal structure of human RAB11-RABIN8-FIP3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UJ5
- Type
- protein
- Length
- 668 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-11A; Rab-3A-interacting protein
- UniProt
- P62491, Q96QF0
- Ligands
- GNP, MG, SO4
- Pockets
- 8 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein rab-11A | protein | 173 | 32% helix, 27% strand | P62491 |
| B | RAS-related protein rab-11A | protein | 172 | 28% helix, 27% strand | P62491 |
| C | Rab-3A-interacting protein | protein | 169 | 46% helix, 9% strand | Q96QF0 |
| D | Rab-3A-interacting protein | protein | 154 | 50% helix, 8% strand | Q96QF0 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, C, B, D
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.66 | 0.92 | 19 | empty |
| 2 | 502 | 0.65 | 0.77 | 44 | empty |
| 3 | 474 | 0.61 | 0.75 | 61 | GNP, MG |
| 4 | 279 | 0.54 | 0.76 | 40 | GNP, MG, SO4 |
| 5 | 239 | 0.52 | 0.76 | 30 | empty |
Interfaces
4 interfaces between chains.
- A–C · 685 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 656 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 354 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 166 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4UJ5 · Crystal structure of human Rab11-Rabin8-FIP3 · the same entry in another collection · chain D against D, TM-score 1.00
- Q96QF0 · AlphaFold monomer V2.0 prediction for rab-3A-interacting protein (Q96QF0) · a predicted model of the same protein · chain C against A, TM-score 0.98
- P62491 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-11A (P62491) · a predicted model of the same protein · chain A 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 P62491
- Every structure of UniProt Q96QF0
- Elsewhere: RCSB PDB 4UJ5 · PDBe 4UJ5 · UniProt P62491 · UniProt Q96QF0
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