Research workbench
Crystal structure of human RAB11 in complex with FIP3 rab-binding domain
Analyse Crystal structure of human RAB11 in complex with FIP3 rab-binding domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D7C
- Type
- protein
- Length
- 418 residues
- Chains
- 4
- 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, MG
- Pockets
- 5 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RAS-related protein rab-11A | protein | 167 | 34% helix, 28% strand | P62491 |
| C, D | RAB11 family-interacting protein 3 | protein | 42 | 81% helix, 2% strand | O75154 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.54 | 0.80 | 24 | empty |
| 2 | 257 | 0.53 | 0.76 | 37 | empty |
| 3 | 128 | 0.46 | 0.78 | 27 | MG, GTP |
| 4 | 124 | 0.44 | 0.77 | 26 | MG, GTP |
| 5 | 133 | 0.42 | 0.75 | 23 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1005 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 713 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 687 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 163 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 155 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 2D7C · Crystal structure of human Rab11 in complex with FIP3 Rab-binding domain · the same entry in another collection · chain A against A, 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 0.97
- O75154 · AlphaFold monomer V2.0 prediction for RAB11 family-interacting protein 3 (O75154) · a predicted model of the same protein · chain C against A, TM-score 0.79
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 2D7C · PDBe 2D7C · UniProt P62491 · UniProt O75154
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