Research workbench
Crystal structure of rab GDP dissociation inhibitor alpha from naegleria fowleri
Analyse Crystal structure of rab GDP dissociation inhibitor alpha from naegleria fowleri in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C87
- Type
- protein
- Length
- 1,765 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rab GDP dissociation inhibitor alpha
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rab GDP dissociation inhibitor alpha | protein | 442 | 35% helix, 24% strand | — |
| B, C, D | Rab GDP dissociation inhibitor alpha | protein | 441 | 36% helix, 25% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 802 | 0.71 | 0.77 | 70 | empty |
| 2 | 683 | 0.70 | 0.78 | 67 | empty |
| 3 | 714 | 0.69 | 0.76 | 54 | empty |
| 4 | 611 | 0.67 | 0.77 | 59 | empty |
| 5 | 231 | 0.66 | 0.83 | 51 | empty |
Interfaces
4 interfaces between chains.
- A–C · 678 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 671 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 153 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 71 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6C87 · Crystal structure of rab gdp dissociation inhibitor alpha from Naegleria fowleri · 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
- Elsewhere: RCSB PDB 6C87 · PDBe 6C87
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