MolNFT v1 · #137296 · protein
Crystal structure of a phosphoribosylformylglycinamidine cyclo-ligase from neisseria gonorrhoeae bound to amppnp and magnesium
5VK4: “Crystal structure of a phosphoribosylformylglycinamidine cyclo-ligase from neisseria gonorrhoeae bound to…”. X-ray diffraction, 2 ligands (ANP, MG), 6 pockets (best druggability 0.71). MolNFT v1 #137296 on GenesisL1: 3D structure…
- PDB
- 5VK4
- Type
- protein
- Length
- 654 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoribosylformylglycinamidine cyclo-ligase
- EC
- 6.3.3.1
- UniProt
- A0A1D3FYK6
- Ligands
- ANP, MG
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoribosylformylglycinamidine cyclo-ligase (EC 6.3.3.1) | protein | 324 | 38% helix, 26% strand | A0A1D3FYK6 |
| B | Phosphoribosylformylglycinamidine cyclo-ligase (EC 6.3.3.1) | protein | 330 | 37% helix, 26% strand | A0A1D3FYK6 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
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 | 689 | 0.71 | 0.78 | 67 | MG, ANP |
| 2 | 525 | 0.62 | 0.75 | 62 | ANP |
| 3 | 132 | 0.41 | 0.75 | 23 | empty |
| 4 | 72 | 0.35 | 0.76 | 19 | empty |
| 5 | 67 | 0.33 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1981 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 5VK4 · Crystal structure of a phosphoribosylformylglycinamidine cyclo-ligase from Neisseria… · 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 A0A1D3FYK6
- Elsewhere: RCSB PDB 5VK4 · PDBe 5VK4 · UniProt A0A1D3FYK6
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