MolNFT v1 · #12038 · protein
Crystal structure of E. COLI nicotinic acid mononucleotide adenylyltransferase
1K4K: “Crystal structure of E. COLI nicotinic acid mononucleotide adenylyltransferase”. X-ray diffraction, 1 ligand (XE), 7 pockets (best druggability 0.77). MolNFT v1 #12038 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1K4K
- Type
- protein
- Length
- 842 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinic acid mononucleotide adenylyltransferase
- EC
- 2.7.7.18
- UniProt
- P0A752
- Ligands
- XE
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Nicotinic acid mononucleotide adenylyltransferase (EC 2.7.7.18) | protein | 213 | 41% helix, 15% strand | P0A752 |
| B | Nicotinic acid mononucleotide adenylyltransferase (EC 2.7.7.18) | protein | 204 | 37% helix, 16% strand | P0A752 |
| D | Nicotinic acid mononucleotide adenylyltransferase (EC 2.7.7.18) | protein | 212 | 43% helix, 15% strand | P0A752 |
Ligands and binding sites
- XE · Xenon · ion · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1042 | 0.77 | 0.79 | 100 | empty |
| 2 | 557 | 0.75 | 0.82 | 61 | XE |
| 3 | 712 | 0.73 | 0.79 | 55 | empty |
| 4 | 619 | 0.71 | 0.79 | 59 | XE |
| 5 | 670 | 0.70 | 0.78 | 55 | XE |
Interfaces
5 interfaces between chains.
- B–D · 435 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 408 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 292 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 255 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 81 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1K4K · Crystal structure of E. coli Nicotinic acid mononucleotide adenylyltransferase · 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 B against A, TM-score 0.96
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 1K4K · PDBe 1K4K · UniProt P0A752
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