MolNFT v1 · #111289 · protein
Crystal structure of probable nicotinate-nucleotide adenylyltransferase from mycobacterium abcessus in complex with NADP
4YMI: “Crystal structure of probable nicotinate-nucleotide adenylyltransferase from mycobacterium abcessus in…”. X-ray diffraction, 2 ligands (NAP, ADE), 6 pockets (best druggability 0.71). MolNFT v1 #111289 on GenesisL1: 3D structure…
- PDB
- 4YMI
- Type
- protein
- Length
- 376 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable nicotinate-nucleotide adenylyltransferase
- EC
- 2.7.7.18
- UniProt
- B1MMZ4
- Ligands
- NAP, ADE
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable nicotinate-nucleotide adenylyltransferase (EC 2.7.7.18) | protein | 178 | 42% helix, 21% strand | B1MMZ4 |
| B | Probable nicotinate-nucleotide adenylyltransferase (EC 2.7.7.18) | protein | 198 | 39% helix, 19% strand | B1MMZ4 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- ADE · Adenine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 451 | 0.71 | 0.81 | 45 | NAP |
| 2 | 310 | 0.58 | 0.77 | 39 | NAP |
| 3 | 190 | 0.50 | 0.77 | 26 | ADE |
| 4 | 85 | 0.50 | 0.83 | 21 | empty |
| 5 | 72 | 0.47 | 0.83 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 890 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4YMI · Crystal structure of probable nicotinate-nucleotide adenylyltransferase from… · the same entry in another collection · chain A against A, TM-score 1.00
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 B1MMZ4
- Elsewhere: RCSB PDB 4YMI · PDBe 4YMI · UniProt B1MMZ4
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