MolNFT v1 · #164344 · protein
The RAB33B-ATG16L1 crystal structure
6SUR · RAS-related protein rab-33B: “The RAB33B-ATG16L1 crystal structure”. X-ray diffraction, 2 ligands (GTP, MG), 15 pockets (best druggability 0.62). MolNFT v1 #164344 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6SUR
- Type
- protein
- Length
- 1,319 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-33B; Autophagy-related protein 16-1
- UniProt
- O35963, Q8C0J2
- Ligands
- GTP, MG
- Pockets
- 15 · best druggability 0.62
Structure
x-ray diffraction · 5 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E | RAS-related protein rab-33B | protein | 171 | 35% helix, 24% strand | O35963 |
| D | RAS-related protein rab-33B | protein | 166 | 33% helix, 27% strand | O35963 |
| F | RAS-related protein rab-33B | protein | 170 | 34% helix, 25% strand | O35963 |
| I, J, K, L, M | Autophagy-related protein 16-1 | protein | 50 | 94% helix, 0% strand | Q8C0J2 |
| N | Autophagy-related protein 16-1 | protein | 49 | 94% helix, 0% strand | Q8C0J2 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 347 | 0.62 | 0.79 | 43 | empty |
| 2 | 330 | 0.54 | 0.75 | 26 | empty |
| 3 | 282 | 0.52 | 0.75 | 26 | empty |
| 4 | 299 | 0.52 | 0.74 | 25 | empty |
| 5 | 272 | 0.52 | 0.75 | 23 | empty |
Interfaces
19 interfaces between chains.
- I–J · 1128 Ų buried · 5 hydrogen bonds · protein-protein
- M–N · 1121 Ų buried · 6 hydrogen bonds · protein-protein
- K–L · 1086 Ų buried · 3 hydrogen bonds · protein-protein
- F–N · 589 Ų buried · 5 hydrogen bonds · protein-protein
- B–J · 583 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6SUR · The Rab33B-Atg16L1 crystal structure · the same entry in another collection · chain N against N, 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 O35963
- Every structure of UniProt Q8C0J2
- Elsewhere: RCSB PDB 6SUR · PDBe 6SUR · UniProt O35963 · UniProt Q8C0J2
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