Research workbench
Crystal structure of E.COLI nicotinic acid mononucleotide adenylyltransferase complexed to deamido-NAD
Analyse Crystal structure of E.COLI nicotinic acid mononucleotide adenylyltransferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1K4M
- Type
- protein
- Length
- 639 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Namn adenylyltransferase
- EC
- 2.7.7.18
- UniProt
- P0A752
- Ligands
- NAD
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Namn adenylyltransferase (EC 2.7.7.18) | protein | 213 | 43% helix, 14% strand | P0A752 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 3 copies · chains A, B, C
- CIT · Citric acid · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 973 | 0.77 | 0.79 | 95 | empty |
| 2 | 433 | 0.74 | 0.84 | 54 | NAD, CIT |
| 3 | 367 | 0.74 | 0.85 | 51 | NAD, CIT |
| 4 | 434 | 0.73 | 0.83 | 55 | NAD, CIT |
| 5 | 124 | 0.51 | 0.81 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–C · 668 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 664 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 637 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1K4M · Crystal structure of E.coli nicotinic acid mononucleotide adenylyltransferase complexed… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A752 · AlphaFold monomer V2.0 prediction for nicotinate-nucleotide adenylyltransferase (P0A752) · 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 P0A752
- Elsewhere: RCSB PDB 1K4M · PDBe 1K4M · UniProt P0A752
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