Research workbench
Crystal structure of NMN/NAMN adenylyltransferase complexed with deamido-NAD
Analyse Crystal structure of NMN/NAMN adenylyltransferase complexed with deamido-NAD in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KQO
- Type
- protein
- Length
- 1,398 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
- DND
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Nicotinamide mononucleotide adenylyl transferase (EC 2.7.7.1) | protein | 233 | 47% helix, 18% strand | Q9HAN9 |
Ligands and binding sites
- DND · Nicotinic acid 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
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 | 807 | 0.84 | 0.87 | 62 | empty |
| 2 | 697 | 0.82 | 0.86 | 60 | empty |
| 3 | 754 | 0.81 | 0.84 | 61 | empty |
| 4 | 513 | 0.73 | 0.81 | 49 | DND |
| 5 | 481 | 0.72 | 0.81 | 50 | DND |
Interfaces
12 interfaces between chains.
- E–F · 1158 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1137 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1131 Ų buried · 20 hydrogen bonds · protein-protein
- D–F · 568 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 543 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1KQO · Crystal structure of NMN/NaMN adenylyltransferase complexed with deamido-NAD · the same entry in another collection · chain B against B, 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 0.98
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 1KQO · PDBe 1KQO · UniProt Q9HAN9
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