MolNFT v1 · #160012 · protein
Structure of P. aeruginosa ATCC27853 cdnd, apo form 1
6P82 · Nucleotidyltransferase: “Structure of P. aeruginosa ATCC27853 cdnd, apo form 1”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.79). MolNFT v1 #160012 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6P82
- Type
- protein
- Length
- 1,205 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleotidyltransferase
- UniProt
- A0A080VY32
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleotidyltransferase | protein | 300 | 51% helix, 13% strand | A0A080VY32 |
| B, C | Nucleotidyltransferase | protein | 302 | 51% helix, 13% strand | A0A080VY32 |
| D | Nucleotidyltransferase | protein | 301 | 50% helix, 13% strand | A0A080VY32 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 34 copies · chains A, B, C, 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 | 975 | 0.79 | 0.80 | 70 | SO4 |
| 2 | 798 | 0.77 | 0.81 | 71 | SO4 |
| 3 | 728 | 0.75 | 0.80 | 57 | SO4 |
| 4 | 686 | 0.74 | 0.80 | 58 | SO4 |
| 5 | 279 | 0.72 | 0.86 | 35 | empty |
Interfaces
4 interfaces between chains.
- A–C · 953 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 428 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 357 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 232 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 6P82 · Structure of P. aeruginosa ATCC27853 CdnD, Apo form 1 · 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 A0A080VY32
- Elsewhere: RCSB PDB 6P82 · PDBe 6P82 · UniProt A0A080VY32
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