MolNFT v1 · #12754 · protein
Crystal structure of NMN/NAMN adenylyltransferase complexed with NAD
1KQN · Nicotinamide mononucleotide adenylyl transferase: “Crystal structure of NMN/NAMN adenylyltransferase complexed with NAD”. X-ray diffraction, 2 ligands (NAD, XE), 13 pockets (best druggability 0.83). MolNFT v1 #12754 on GenesisL1: 3D…
- PDB
- 1KQN
- Type
- protein
- Length
- 1,388 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
- NAD, XE
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Nicotinamide mononucleotide adenylyl transferase (EC 2.7.7.1) | protein | 232 | 47% helix, 18% strand | Q9HAN9 |
| B, C, D, F | Nicotinamide mononucleotide adenylyl transferase (EC 2.7.7.1) | protein | 231 | 48% helix, 18% strand | Q9HAN9 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 6 copies · chains A, B, C, D, E, F
- XE · Xenon · ion · 15 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 837 | 0.83 | 0.86 | 73 | XE |
| 2 | 825 | 0.83 | 0.86 | 70 | XE |
| 3 | 839 | 0.82 | 0.84 | 72 | XE |
| 4 | 506 | 0.73 | 0.82 | 58 | NAD, XE |
| 5 | 502 | 0.72 | 0.81 | 44 | NAD, XE |
Interfaces
12 interfaces between chains.
- E–F · 1172 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1118 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1116 Ų buried · 22 hydrogen bonds · protein-protein
- B–E · 572 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 568 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1KQN · Crystal structure of NMN/NaMN adenylyltransferase complexed with NAD · 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 B against A, TM-score 0.98
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 1KQN · PDBe 1KQN · UniProt Q9HAN9
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