Research workbench
Crystal structure of nicotinic acid mononucleotide adenylyltransferase from pseudomonas aeruginosa
Analyse Crystal structure of nicotinic acid mononucleotide adenylyltransferase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YUM
- Type
- protein
- Length
- 848 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 'probable nicotinate-nucleotide adenylyltransferase
- EC
- 2.7.7.18
- UniProt
- Q9HX21
- Ligands
- NCN
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 'probable nicotinate-nucleotide adenylyltransferase (EC 2.7.7.18) | protein | 212 | 40% helix, 17% strand | Q9HX21 |
Ligands and binding sites
- NCN · Nicotinate mononucleotide · ligand · 4 copies · chains A, B, C, D
- CIT · Citric acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 801 | 0.73 | 0.78 | 69 | empty |
| 2 | 637 | 0.71 | 0.79 | 52 | empty |
| 3 | 354 | 0.59 | 0.76 | 40 | CIT, NCN |
| 4 | 329 | 0.58 | 0.76 | 41 | CIT, NCN |
| 5 | 301 | 0.58 | 0.77 | 38 | CIT, NCN |
Interfaces
6 interfaces between chains.
- B–D · 1003 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 309 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 296 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 202 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 201 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1YUM · Crystal Structure of Nicotinic Acid Mononucleotide Adenylyltransferase from Pseudomonas… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HX21 · AlphaFold monomer V2.0 prediction for probable nicotinate-nucleotide adenylyltransferase… · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q9HX21
- Elsewhere: RCSB PDB 1YUM · PDBe 1YUM · UniProt Q9HX21
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