MolNFT v1 · #78032 · protein
Crystal structure of YPT32 in complex with GDP
3RWO · GTP-binding protein YPT32/YPT11: “Crystal structure of YPT32 in complex with GDP”. X-ray diffraction, 2 ligands (GDP, MG), 2 pockets (best druggability 0.76). MolNFT v1 #78032 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3RWO
- Type
- protein
- Length
- 342 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTP-binding protein YPT32/YPT11
- UniProt
- P51996
- Ligands
- GDP, MG
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | GTP-binding protein YPT32/YPT11 | protein | 172 | 38% helix, 28% strand | P51996 |
| A | GTP-binding protein YPT32/YPT11 | protein | 170 | 38% helix, 29% strand | P51996 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains B, A
- MG · Magnesium ion · metal · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1037 | 0.76 | 0.78 | 99 | GDP, MG |
| 2 | 58 | 0.29 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- B–A · 667 Ų buried · 8 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 P51996
- Elsewhere: RCSB PDB 3RWO · PDBe 3RWO · UniProt P51996
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