Research workbench
Lida from legionella in complex with active RAB8A
Analyse Lida from legionella in complex with active RAB8A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TNF
- Type
- protein
- Length
- 549 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-8A; Lida
- UniProt
- P61006, Q5ZWZ3
- Ligands
- GNP, MG
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein rab-8A | protein | 170 | 38% helix, 27% strand | P61006 |
| B | Lida | protein | 379 | 61% helix, 13% strand | Q5ZWZ3 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A, B
- MG · Magnesium ion · metal · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 875 | 0.81 | 0.84 | 88 | MG, GNP |
| 2 | 1136 | 0.73 | 0.77 | 75 | MPD |
| 3 | 119 | 0.68 | 0.90 | 17 | MPD |
| 4 | 65 | 0.60 | 0.90 | 18 | MPD |
| 5 | 211 | 0.50 | 0.75 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1709 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
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 P61006
- Every structure of UniProt Q5ZWZ3
- Elsewhere: RCSB PDB 3TNF · PDBe 3TNF · UniProt P61006 · UniProt Q5ZWZ3
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