MolNFT v1 · #88557 · protein
Complex of human varp-ANKRD1 with RAB32-gppcp
4CYM · RAS-related protein rab-32: “Complex of human varp-ANKRD1 with RAB32-gppcp”. X-ray diffraction, 2 ligands (GCP, MG), 13 pockets (best druggability 0.64). MolNFT v1 #88557 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4CYM
- Type
- protein
- Length
- 1,027 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-32; Ankyrin repeat domain-containing protein 27
- EC
- 3.6.5.2
- UniProt
- Q13637, Q96NW4
- Ligands
- GCP, MG
- Pockets
- 13 · best druggability 0.64
Structure
x-ray diffraction · 5 distinct chains · 42% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | RAS-related protein rab-32 (EC 3.6.5.2) | protein | 177 | 34% helix, 29% strand | Q13637 |
| B | RAS-related protein rab-32 (EC 3.6.5.2) | protein | 175 | 35% helix, 27% strand | Q13637 |
| D | Ankyrin repeat domain-containing protein 27 | protein | 167 | 47% helix, 0% strand | Q96NW4 |
| E | Ankyrin repeat domain-containing protein 27 | protein | 165 | 47% helix, 0% strand | Q96NW4 |
| F | Ankyrin repeat domain-containing protein 27 | protein | 166 | 49% helix, 0% strand | Q96NW4 |
Ligands and binding sites
- GCP · Phosphomethylphosphonic acid guanylate ester · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 406 | 0.64 | 0.78 | 49 | GCP, MG |
| 2 | 406 | 0.62 | 0.77 | 49 | GCP, MG |
| 3 | 366 | 0.62 | 0.78 | 50 | GCP, MG |
| 4 | 442 | 0.57 | 0.74 | 61 | empty |
| 5 | 256 | 0.49 | 0.74 | 28 | empty |
Interfaces
5 interfaces between chains.
- B–E · 840 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 812 Ų buried · 9 hydrogen bonds · protein-protein
- C–F · 771 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 346 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 338 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4CYM · Complex of human VARP-ANKRD1 with Rab32-GppCp · the same entry in another collection · chain F against F, TM-score 1.00
- Q13637 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-32 (Q13637) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q96NW4 · AlphaFold monomer V2.0 prediction for ankyrin repeat domain- containing protein 27… · a predicted model of the same protein · chain F against A, TM-score 0.98
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 Q13637
- Every structure of UniProt Q96NW4
- Elsewhere: RCSB PDB 4CYM · PDBe 4CYM · UniProt Q13637 · UniProt Q96NW4
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