Research workbench
Structure of nmn synthetase from francisella tularensis
Analyse Structure of nmn synthetase from francisella tularensis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FIU
- Type
- protein
- Length
- 952 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NH(3)-dependent NAD(+) synthetase
- EC
- 6.3.1.5
- UniProt
- Q2A4B6
- Ligands
- AMP, POP, MG, NA
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | NH(3)-dependent NAD(+) synthetase (EC 6.3.1.5) | protein | 238 | 55% helix, 8% strand | Q2A4B6 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 4 copies · chains A, B, C, D
- POP · Pyrophosphate 2- · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 695 | 0.83 | 0.87 | 79 | MG, AMP, POP, NA |
| 2 | 834 | 0.83 | 0.85 | 81 | MG, AMP, POP, NA |
| 3 | 836 | 0.82 | 0.85 | 83 | MG, AMP, POP, NA |
| 4 | 908 | 0.82 | 0.84 | 96 | MG, AMP, POP, NA |
| 5 | 190 | 0.77 | 0.92 | 39 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2623 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 2603 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 325 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 274 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 92 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3FIU · Structure of NMN synthetase from Francisella tularensis · 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 Q2A4B6
- Elsewhere: RCSB PDB 3FIU · PDBe 3FIU · UniProt Q2A4B6
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