MolNFT v1 · #171616 · protein
Crystal structure of ATG16L in complex with GDP-bound RAB33B
6ZAY · RAS-related protein rab-33B: “Crystal structure of ATG16L in complex with GDP-bound RAB33B”. X-ray diffraction, 3 ligands (GDP, MG, PO4), 7 pockets (best druggability 0.52). MolNFT v1 #171616 on GenesisL1: 3D structure, binding…
- PDB
- 6ZAY
- Type
- protein
- Length
- 522 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-33B; Autophagy-related protein 16-1
- UniProt
- Q9H082, Q8C0J2
- Ligands
- GDP, MG, PO4
- Pockets
- 7 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RAS-related protein rab-33B | protein | 175 | 35% helix, 25% strand | Q9H082 |
| C, D | Autophagy-related protein 16-1 | protein | 86 | 86% helix, 0% strand | Q8C0J2 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 5 copies · chains A, C, D, B
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 198 | 0.52 | 0.77 | 31 | empty |
| 2 | 203 | 0.48 | 0.75 | 25 | PO4 |
| 3 | 141 | 0.46 | 0.77 | 22 | empty |
| 4 | 107 | 0.45 | 0.79 | 24 | MG, GDP |
| 5 | 100 | 0.43 | 0.78 | 25 | MG, GDP |
Interfaces
5 interfaces between chains.
- C–D · 1094 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 934 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 827 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 191 Ų buried · 4 hydrogen bonds · protein-protein
- C–B · 190 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6ZAY · Crystal structure of Atg16L in complex with GDP-bound Rab33B · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H082 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-33B (Q9H082) · a predicted model of the same protein · chain A against A, TM-score 0.95
- Q8C0J2 · AlphaFold monomer V2.0 prediction for autophagy-related protein 16-1 (Q8C0J2) · a predicted model of the same protein · chain C against A, TM-score 0.86
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 Q9H082
- Every structure of UniProt Q8C0J2
- Elsewhere: RCSB PDB 6ZAY · PDBe 6ZAY · UniProt Q9H082 · UniProt Q8C0J2
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