MolNFT v1 · #50444 · protein
Cbs domain protein PAE2072 from pyrobaculum aerophilum complexed with AMP
2RIF · Conserved protein with 2 cbs domains: “Cbs domain protein PAE2072 from pyrobaculum aerophilum complexed with AMP”. X-ray diffraction, 2 ligands (AMP, CS), 8 pockets (best druggability 0.85). MolNFT v1 #50444 on GenesisL1: 3D…
- PDB
- 2RIF
- Type
- protein
- Length
- 518 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Conserved protein with 2 cbs domains
- UniProt
- Q8ZVX8
- Ligands
- AMP, CS
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Conserved protein with 2 cbs domains | protein | 131 | 39% helix, 25% strand | Q8ZVX8 |
| B | Conserved protein with 2 cbs domains | protein | 129 | 39% helix, 26% strand | Q8ZVX8 |
| C | Conserved protein with 2 cbs domains | protein | 128 | 38% helix, 26% strand | Q8ZVX8 |
| D | Conserved protein with 2 cbs domains | protein | 130 | 38% helix, 25% strand | Q8ZVX8 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 8 copies · chains A, B, D, C
- CS · Cesium ion · metal · 11 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1152 | 0.85 | 0.86 | 98 | CS, AMP |
| 2 | 306 | 0.68 | 0.82 | 38 | AMP |
| 3 | 167 | 0.58 | 0.82 | 23 | AMP |
| 4 | 155 | 0.53 | 0.80 | 19 | AMP |
| 5 | 63 | 0.51 | 0.85 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1790 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1748 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 450 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 357 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 326 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2RIF · CBS domain protein PAE2072 from Pyrobaculum aerophilum complexed with AMP · 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 Q8ZVX8
- Elsewhere: RCSB PDB 2RIF · PDBe 2RIF · UniProt Q8ZVX8
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