Research workbench
Crystal structure of plasmodium falciparum RAB11A in complex with GDP
Analyse Crystal structure of plasmodium falciparum RAB11A in complex with GDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BFK
- Type
- protein
- Length
- 824 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Small GTPase RAB11
- EC
- 3.6.5.2
- UniProt
- Q76NM4
- Ligands
- GDP
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 38% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Small GTPase RAB11 (EC 3.6.5.2) | protein | 159 | 38% helix, 28% strand | Q76NM4 |
| B | Small GTPase RAB11 (EC 3.6.5.2) | protein | 179 | 37% helix, 25% strand | Q76NM4 |
| C | Small GTPase RAB11 (EC 3.6.5.2) | protein | 170 | 41% helix, 26% strand | Q76NM4 |
| D | Small GTPase RAB11 (EC 3.6.5.2) | protein | 159 | 39% helix, 28% strand | Q76NM4 |
| E | Small GTPase RAB11 (EC 3.6.5.2) | protein | 157 | 38% helix, 29% strand | Q76NM4 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 5 copies · chains A, C, B, D, E
- GOL · Glycerol · additive · 3 copies · chains B, C, D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 994 | 0.81 | 0.82 | 87 | GOL |
| 2 | 493 | 0.65 | 0.77 | 60 | GDP |
| 3 | 346 | 0.58 | 0.76 | 46 | empty |
| 4 | 140 | 0.52 | 0.81 | 27 | GDP |
| 5 | 163 | 0.48 | 0.77 | 28 | empty |
Interfaces
6 interfaces between chains.
- A–B · 874 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 787 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 641 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 546 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 508 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3BFK · Crystal structure of Plasmodium falciparum Rab11a in complex with GDP · the same entry in another collection · chain A against A, 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 Q76NM4
- Elsewhere: RCSB PDB 3BFK · PDBe 3BFK · UniProt Q76NM4
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