MolNFT v1 · #119109 · protein
Double-heterohexameric rings of full-length RVB1(ADP)RVB2(APO)
5FM6: “Double-heterohexameric rings of full-length RVB1(ADP)RVB2(APO)”. X-ray diffraction, 2 ligands (ADP, PO4), 13 pockets (best druggability 0.71). MolNFT v1 #119109 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5FM6
- Type
- protein
- Length
- 845 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RVB1; RVB2
- UniProt
- G0RYI5, G0RYC2
- Ligands
- ADP, PO4
- Pockets
- 13 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RVB1 | protein | 426 | 36% helix, 21% strand | G0RYI5 |
| B | RVB2 | protein | 419 | 37% helix, 22% strand | G0RYC2 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 470 | 0.71 | 0.81 | 58 | PO4 |
| 2 | 550 | 0.68 | 0.78 | 63 | empty |
| 3 | 310 | 0.68 | 0.83 | 46 | empty |
| 4 | 164 | 0.68 | 0.87 | 24 | ADP |
| 5 | 159 | 0.58 | 0.82 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 2360 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 modified (engineered).
Compared structures
- 5FM6 · Double-heterohexameric rings of full-length Rvb1(ADP)Rvb2(apo) · the same entry in another collection · chain A against A, 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 G0RYI5
- Every structure of UniProt G0RYC2
- Elsewhere: RCSB PDB 5FM6 · PDBe 5FM6 · UniProt G0RYI5 · UniProt G0RYC2
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