MolNFT v1 · #126591 · protein
Crystal structure of bacillus subtilis enga in complex with phosphate ion and gmppnp
5M7H · GTPase der: “Crystal structure of bacillus subtilis enga in complex with phosphate ion and gmppnp”. X-ray diffraction, 3 ligands (GNP, K, PO4), 6 pockets (best druggability 0.73). MolNFT v1 #126591 on GenesisL1: 3D structure…
- PDB
- 5M7H
- Type
- protein
- Length
- 420 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase der
- UniProt
- P50743
- Ligands
- GNP, K, PO4
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase der | protein | 420 | 35% helix, 23% strand | P50743 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
- K · Potassium ion · metal · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 620 | 0.73 | 0.80 | 52 | empty |
| 2 | 208 | 0.66 | 0.85 | 35 | GNP |
| 3 | 59 | 0.43 | 0.82 | 18 | empty |
| 4 | 130 | 0.40 | 0.74 | 19 | empty |
| 5 | 77 | 0.35 | 0.76 | 15 | empty |
Compared structures
- 5M7H · Crystal structure of Bacillus subtilis EngA in complex with phosphate ion and GMPPNP · the same entry in another collection · chain A against A, TM-score 1.00
- P50743 · AlphaFold monomer V2.0 prediction for GTPase der (P50743) · a predicted model of the same protein · chain A against A, TM-score 0.62
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 P50743
- Elsewhere: RCSB PDB 5M7H · PDBe 5M7H · UniProt P50743
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