MolNFT v1 · #113889 · protein
Crystal structures of 5-aminoimidazole ribonucleotide (air) synthetase, purm, from thermus thermophilus
5AVM · Phosphoribosylformylglycinamidine cyclo-ligase: “Crystal structures of 5-aminoimidazole ribonucleotide (air) synthetase, purm, from thermus thermophilus”. X-ray diffraction, 1 ligand (SO4), 17 pockets (best druggability 0.69).…
- PDB
- 5AVM
- Type
- protein
- Length
- 2,256 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoribosylformylglycinamidine cyclo-ligase
- EC
- 6.3.3.1
- UniProt
- Q5SLC6
- Ligands
- SO4
- Pockets
- 17 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Phosphoribosylformylglycinamidine cyclo-ligase (EC 6.3.3.1) | protein | 281 | 34% helix, 26% strand | Q5SLC6 |
| B, D, F, H | Phosphoribosylformylglycinamidine cyclo-ligase (EC 6.3.3.1) | protein | 283 | 36% helix, 26% strand | Q5SLC6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 17 copies · chains A, B, C, D, E, H, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 765 | 0.69 | 0.76 | 77 | SO4 |
| 2 | 697 | 0.69 | 0.77 | 78 | SO4 |
| 3 | 603 | 0.68 | 0.77 | 60 | SO4 |
| 4 | 470 | 0.66 | 0.78 | 48 | SO4 |
| 5 | 541 | 0.66 | 0.77 | 57 | SO4 |
Interfaces
15 interfaces between chains.
- A–B · 1324 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1303 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1287 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 1284 Ų buried · 12 hydrogen bonds · protein-protein
- E–G · 717 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5AVM · Crystal structures of 5-aminoimidazole ribonucleotide (AIR) synthetase, PurM, from… · 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 Q5SLC6
- Elsewhere: RCSB PDB 5AVM · PDBe 5AVM · UniProt Q5SLC6
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