MolNFT v1 · #65118 · protein
Crystal structure of nicotinate-nucleotide pyrophosphorylase from burkholderi pseudomallei
3GNN: “Crystal structure of nicotinate-nucleotide pyrophosphorylase from burkholderi pseudomallei”. X-ray diffraction, 3 pockets (best druggability 0.77). MolNFT v1 #65118 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3GNN
- Type
- protein
- Length
- 518 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinate-nucleotide pyrophosphorylase; Unknown peptide
- EC
- 2.4.2.19
- UniProt
- Q3JV59
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicotinate-nucleotide pyrophosphorylase (EC 2.4.2.19) | protein | 266 | 46% helix, 19% strand | Q3JV59 |
| B | Nicotinate-nucleotide pyrophosphorylase (EC 2.4.2.19) | protein | 244 | 43% helix, 19% strand | Q3JV59 |
| D, E | Unknown peptide | protein | 4 | 0% helix, 50% strand | — |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 749 | 0.77 | 0.81 | 63 | empty |
| 2 | 952 | 0.73 | 0.77 | 68 | empty |
| 3 | 132 | 0.44 | 0.76 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1411 Ų buried · 26 hydrogen bonds · protein-protein
- B–E · 184 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 182 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 40 Ų buried · 0 hydrogen bonds · protein-protein
- A–E · 18 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3GNN · Crystal structure of nicotinate-nucleotide pyrophosphorylase from Burkholderi pseudomallei · 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 Q3JV59
- Elsewhere: RCSB PDB 3GNN · PDBe 3GNN · UniProt Q3JV59
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