MolNFT v1 · #116461 · protein
Crystal structure of the small alarmone synthethase 1 from bacillus subtilis bound to its product pppgpp
5DED · GTP pyrophosphokinase yjbm: “Crystal structure of the small alarmone synthethase 1 from bacillus subtilis bound to its product pppgpp”. X-ray diffraction, 2 ligands (0O2, MG), 20 pockets (best druggability 0.74). MolNFT v1 #116461…
- PDB
- 5DED
- Type
- protein
- Length
- 1,535 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTP pyrophosphokinase yjbm
- EC
- 2.7.6.5
- UniProt
- O31611
- Ligands
- 0O2, MG
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 8 distinct chains · 49% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | GTP pyrophosphokinase yjbm (EC 2.7.6.5) | protein | 188 | 49% helix, 22% strand | O31611 |
| A | GTP pyrophosphokinase yjbm (EC 2.7.6.5) | protein | 196 | 51% helix, 21% strand | O31611 |
| B | GTP pyrophosphokinase yjbm (EC 2.7.6.5) | protein | 191 | 48% helix, 22% strand | O31611 |
| C | GTP pyrophosphokinase yjbm (EC 2.7.6.5) | protein | 194 | 49% helix, 22% strand | O31611 |
| E | GTP pyrophosphokinase yjbm (EC 2.7.6.5) | protein | 190 | 53% helix, 20% strand | O31611 |
| F | GTP pyrophosphokinase yjbm (EC 2.7.6.5) | protein | 192 | 45% helix, 21% strand | O31611 |
| G | GTP pyrophosphokinase yjbm (EC 2.7.6.5) | protein | 190 | 49% helix, 22% strand | O31611 |
| H | GTP pyrophosphokinase yjbm (EC 2.7.6.5) | protein | 194 | 51% helix, 21% strand | O31611 |
Ligands and binding sites
- 0O2 · guanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate) · ligand · 12 copies · chains D, B, A, C, E, F, G, H
- MG · Magnesium ion · metal · 4 copies · chains A, C, D, B, E, H, 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1129 | 0.74 | 0.77 | 79 | 0O2 |
| 2 | 969 | 0.74 | 0.77 | 58 | 0O2 |
| 3 | 987 | 0.72 | 0.76 | 68 | 0O2 |
| 4 | 991 | 0.72 | 0.76 | 59 | 0O2 |
| 5 | 620 | 0.69 | 0.78 | 63 | 0O2 |
Interfaces
9 interfaces between chains.
- A–C · 1693 Ų buried · 8 hydrogen bonds · protein-protein
- D–B · 1587 Ų buried · 13 hydrogen bonds · protein-protein
- E–H · 1552 Ų buried · 12 hydrogen bonds · protein-protein
- F–G · 1490 Ų buried · 7 hydrogen bonds · protein-protein
- D–F · 1134 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5DED · Crystal structure of the small alarmone synthethase 1 from Bacillus subtilis bound to its… · the same entry in another collection · chain H against H, TM-score 1.00
- O31611 · AlphaFold monomer V2.0 prediction for GTP pyrophosphokinase yjbm (O31611) · a predicted model of the same protein · chain G 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 O31611
- Elsewhere: RCSB PDB 5DED · PDBe 5DED · UniProt O31611
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