MolNFT v1 · #160029 · protein
Structure of P. aeruginosa ATCC27853 cdnd D62N/D64N mutant bound to ATP
6P8J · Nucleotidyltransferase: “Structure of P. aeruginosa ATCC27853 cdnd D62N/D64N mutant bound to ATP”. X-ray diffraction, 3 ligands (ATP, MG, CL), 9 pockets (best druggability 0.80). MolNFT v1 #160029 on GenesisL1: 3D structure, binding…
- PDB
- 6P8J
- Type
- protein
- Length
- 1,200 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleotidyltransferase
- UniProt
- A0A080VY32
- Ligands
- ATP, MG, CL
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A, B, D | Nucleotidyltransferase | protein | 300 | 52% helix, 13% strand | A0A080VY32 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains C, A, B, D
- MG · Magnesium ion · metal · 4 copies · chains C, A, B, D
- CL · Chloride ion · ion · 4 copies · chains C, A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 944 | 0.80 | 0.82 | 88 | ATP, CL, MG |
| 2 | 827 | 0.78 | 0.82 | 69 | ATP, CL, MG |
| 3 | 575 | 0.78 | 0.84 | 51 | ATP, CL, MG |
| 4 | 629 | 0.77 | 0.83 | 58 | ATP, CL, MG |
| 5 | 561 | 0.74 | 0.82 | 70 | empty |
Interfaces
3 interfaces between chains.
- A–B · 985 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 769 Ų buried · 18 hydrogen bonds · protein-protein
- C–A · 530 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6P8J · Structure of P. aeruginosa ATCC27853 CdnD D62N/D64N mutant bound to ATP · the same entry in another collection · chain C against C, 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 A0A080VY32
- Elsewhere: RCSB PDB 6P8J · PDBe 6P8J · UniProt A0A080VY32
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.