Research workbench
Crystal structure of GTP-bound RAB11 in complex with FIP3
Analyse Crystal structure of GTP-bound RAB11 in complex with FIP3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HV8
- Type
- protein
- Length
- 657 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-11A; RAB11 family-interacting protein 3
- UniProt
- P62491, O75154
- Ligands
- GTP, 2ME, MG, SO4
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 55% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | RAS-related protein rab-11A | protein | 169 | 33% helix, 27% strand | P62491 |
| D | RAB11 family-interacting protein 3 | protein | 54 | 74% helix, 2% strand | O75154 |
| E | RAB11 family-interacting protein 3 | protein | 55 | 85% helix, 2% strand | O75154 |
| F | RAB11 family-interacting protein 3 | protein | 41 | 83% helix, 2% strand | O75154 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, B, C
- 2ME · Methoxyethane · ligand · chains B
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, E, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 558 | 0.69 | 0.78 | 54 | MES |
| 2 | 60 | 0.49 | 0.86 | 21 | SO4 |
| 3 | 116 | 0.47 | 0.79 | 25 | MG, GTP |
| 4 | 127 | 0.46 | 0.78 | 23 | SO4 |
| 5 | 118 | 0.46 | 0.78 | 15 | empty |
Interfaces
10 interfaces between chains.
- E–F · 802 Ų buried · 9 hydrogen bonds · protein-protein
- C–F · 768 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 759 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 739 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 423 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2HV8 · Crystal structure of GTP-bound Rab11 in complex with FIP3 · the same entry in another collection · chain E against E, TM-score 1.00
- 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 0.96
- O75154 · AlphaFold monomer V2.0 prediction for RAB11 family-interacting protein 3 (O75154) · a predicted model of the same protein · chain F against A, TM-score 0.71
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 O75154
- Elsewhere: RCSB PDB 2HV8 · PDBe 2HV8 · UniProt P62491 · UniProt O75154
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