MolNFT v1 · #126626 · protein
ATP phosphoribosyltransferase (hiszg atpprt) from psychrobacter arcticus
5M8H · ATP phosphoribosyltransferase regulatory subunit: “ATP phosphoribosyltransferase (hiszg atpprt) from psychrobacter arcticus”. X-ray diffraction, 2 ligands (SR, CL), 20 pockets (best druggability 0.87). MolNFT v1 #126626 on…
- PDB
- 5M8H
- Type
- protein
- Length
- 2,343 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP phosphoribosyltransferase regulatory subunit; ATP phosphoribosyltransferase
- EC
- 2.4.2.17
- UniProt
- Q4FTX3, Q4FQF7
- Ligands
- SR, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP phosphoribosyltransferase regulatory subunit | protein | 377 | 41% helix, 21% strand | Q4FTX3 |
| B, D | ATP phosphoribosyltransferase regulatory subunit | protein | 378 | 41% helix, 22% strand | Q4FTX3 |
| C | ATP phosphoribosyltransferase regulatory subunit | protein | 377 | 41% helix, 22% strand | Q4FTX3 |
| E | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 208 | 33% helix, 33% strand | Q4FQF7 |
| F, H | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 209 | 33% helix, 33% strand | Q4FQF7 |
| G | ATP phosphoribosyltransferase (EC 2.4.2.17) | protein | 207 | 32% helix, 33% strand | Q4FQF7 |
Ligands and binding sites
- SR · Strontium ion · metal · 10 copies · chains A, B, C, D
- CL · Chloride ion · ion · 15 copies · chains A, B, C, D, E, F, G, H
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 12 copies · chains A, B, F, C, H, D, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 999 | 0.87 | 0.88 | 140 | SR, MPD |
| 2 | 962 | 0.87 | 0.88 | 144 | SR, CL, MPD |
| 3 | 687 | 0.80 | 0.85 | 72 | SR, MPD |
| 4 | 494 | 0.78 | 0.85 | 56 | SR, CL, MPD |
| 5 | 1031 | 0.77 | 0.79 | 66 | empty |
Interfaces
20 interfaces between chains.
- A–C · 3237 Ų buried · 42 hydrogen bonds · protein-protein
- B–D · 3210 Ų buried · 39 hydrogen bonds · protein-protein
- F–G · 1298 Ų buried · 8 hydrogen bonds · protein-protein
- E–H · 1253 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 949 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5M8H · ATP phosphoribosyltransferase (HisZG ATPPRT) from Psychrobacter arcticus · the same entry in another collection · chain H against H, TM-score 1.00
- Q4FQF7 · AlphaFold monomer V2.0 prediction for ATP phosphoribosyltransferase (Q4FQF7) · a predicted model of the same protein · chain F against A, TM-score 0.99
- Q4FTX3 · AlphaFold monomer V2.0 prediction for ATP phosphoribosyltransferase regulatory subunit… · a predicted model of the same protein · chain C 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 Q4FTX3
- Every structure of UniProt Q4FQF7
- Elsewhere: RCSB PDB 5M8H · PDBe 5M8H · UniProt Q4FTX3 · UniProt Q4FQF7
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