MolNFT v1 · #12768 · protein
Crystal structure of human NMN/NAMN adenylyl transferase complexed with tiazofurin adenine dinucleotide (tad)
1KR2 · Nicotinamide mononucleotide adenylyl transferase: “Crystal structure of human NMN/NAMN adenylyl transferase complexed with tiazofurin adenine dinucleotide (tad)”. X-ray diffraction, 1 ligand (TAD), 16 pockets (best druggability…
- PDB
- 1KR2
- Type
- protein
- Length
- 1,395 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinamide mononucleotide adenylyl transferase
- EC
- 2.7.7.1
- UniProt
- Q9HAN9
- Ligands
- TAD
- Pockets
- 16 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Nicotinamide mononucleotide adenylyl transferase (EC 2.7.7.1) | protein | 233 | 48% helix, 18% strand | Q9HAN9 |
| E | Nicotinamide mononucleotide adenylyl transferase (EC 2.7.7.1) | protein | 232 | 48% helix, 18% strand | Q9HAN9 |
| F | Nicotinamide mononucleotide adenylyl transferase (EC 2.7.7.1) | protein | 231 | 48% helix, 18% strand | Q9HAN9 |
Ligands and binding sites
- TAD · Beta-methylene-thiazole-4-carboxyamide-adenine dinucleotide · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1195 | 0.84 | 0.85 | 116 | TAD |
| 2 | 735 | 0.83 | 0.86 | 68 | empty |
| 3 | 787 | 0.80 | 0.83 | 62 | empty |
| 4 | 526 | 0.74 | 0.82 | 54 | TAD |
| 5 | 547 | 0.74 | 0.81 | 49 | TAD |
Interfaces
12 interfaces between chains.
- C–D · 1182 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1145 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1132 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 570 Ų buried · 0 hydrogen bonds · protein-protein
- D–F · 564 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1KR2 · Crystal structure of human NMN/NAMN adenylyl transferase complexed with tiazofurin… · the same entry in another collection · chain F against F, TM-score 1.00
- Q9HAN9 · AlphaFold monomer V2.0 prediction for NICOTINAMIDE/NICOTINIC acid mononucleotide… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9HAN9
- Elsewhere: RCSB PDB 1KR2 · PDBe 1KR2 · UniProt Q9HAN9
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