MolNFT v1 · #118474 · protein
Crystal structure of the small alarmone synthethase 1 from bacillus subtilis bound to ampcpp
5F2V · GTP pyrophosphokinase yjbm: “Crystal structure of the small alarmone synthethase 1 from bacillus subtilis bound to ampcpp”. X-ray diffraction, 2 ligands (APC, MG), 20 pockets (best druggability 0.73). MolNFT v1 #118474 on GenesisL1…
- PDB
- 5F2V
- Type
- protein
- Length
- 2,202 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTP pyrophosphokinase yjbm
- EC
- 2.7.6.5
- UniProt
- O31611
- Ligands
- APC, MG
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 11 distinct chains · 54% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| V | GTP pyrophosphokinase yjbm (EC 2.7.6.5) | protein | 180 | 56% helix, 22% strand | O31611 |
| X | GTP pyrophosphokinase yjbm (EC 2.7.6.5) | protein | 181 | 52% helix, 22% strand | O31611 |
| T | GTP pyrophosphokinase yjbm (EC 2.7.6.5) | protein | 195 | 55% helix, 21% strand | O31611 |
| S | GTP pyrophosphokinase yjbm (EC 2.7.6.5) | protein | 182 | 54% helix, 21% strand | O31611 |
| Y | GTP pyrophosphokinase yjbm (EC 2.7.6.5) | protein | 182 | 55% helix, 23% strand | O31611 |
| O, R | GTP pyrophosphokinase yjbm (EC 2.7.6.5) | protein | 184 | 54% helix, 22% strand | O31611 |
| Z | GTP pyrophosphokinase yjbm (EC 2.7.6.5) | protein | 179 | 54% helix, 21% strand | O31611 |
| W | GTP pyrophosphokinase yjbm (EC 2.7.6.5) | protein | 187 | 53% helix, 21% strand | O31611 |
| U | GTP pyrophosphokinase yjbm (EC 2.7.6.5) | protein | 186 | 57% helix, 22% strand | O31611 |
| P | GTP pyrophosphokinase yjbm (EC 2.7.6.5) | protein | 183 | 54% helix, 22% strand | O31611 |
| Q | GTP pyrophosphokinase yjbm (EC 2.7.6.5) | protein | 179 | 53% helix, 21% strand | O31611 |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 12 copies · chains V, X, T, S, Y, O, Z, W, U, P, R, Q
- MG · Magnesium ion · metal · 12 copies · chains V, X, T, S, Y, O, Z, W, U, P, R, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 953 | 0.73 | 0.77 | 86 | APC, MG |
| 2 | 1057 | 0.73 | 0.77 | 102 | APC, MG |
| 3 | 897 | 0.73 | 0.77 | 82 | APC, MG |
| 4 | 934 | 0.72 | 0.76 | 81 | APC, MG |
| 5 | 427 | 0.70 | 0.81 | 49 | empty |
Interfaces
14 interfaces between chains.
- O–P · 1478 Ų buried · 10 hydrogen bonds · protein-protein
- Y–Z · 1471 Ų buried · 11 hydrogen bonds · protein-protein
- T–S · 1444 Ų buried · 10 hydrogen bonds · protein-protein
- R–Q · 1443 Ų buried · 6 hydrogen bonds · protein-protein
- X–W · 1376 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5F2V · Crystal structure of the small alarmone synthethase 1 from Bacillus subtilis bound to… · the same entry in another collection · chain Q against Q, 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 O31611
- Elsewhere: RCSB PDB 5F2V · PDBe 5F2V · UniProt O31611
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