MolNFT v1 · #110939 · protein
Structure of mycobacterium tuberculosis nadd in complex with NADP, P21212
4YBR · Nicotinate-nucleotide adenylyltransferase: “Structure of mycobacterium tuberculosis nadd in complex with NADP, P21212”. X-ray diffraction, 3 ligands (NAP, SO4, CL), 8 pockets (best druggability 0.66). MolNFT v1 #110939 on GenesisL1…
- PDB
- 4YBR
- Type
- protein
- Length
- 393 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinate-nucleotide adenylyltransferase
- EC
- 2.7.7.18
- UniProt
- P9WJJ5
- Ligands
- NAP, SO4, CL
- Pockets
- 8 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicotinate-nucleotide adenylyltransferase (EC 2.7.7.18) | protein | 197 | 50% helix, 18% strand | P9WJJ5 |
| B | Nicotinate-nucleotide adenylyltransferase (EC 2.7.7.18) | protein | 196 | 44% helix, 18% strand | P9WJJ5 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 441 | 0.66 | 0.79 | 47 | NAP, SO4 |
| 2 | 475 | 0.63 | 0.77 | 46 | NAP |
| 3 | 58 | 0.50 | 0.86 | 15 | empty |
| 4 | 57 | 0.45 | 0.84 | 15 | empty |
| 5 | 174 | 0.45 | 0.74 | 34 | EPE |
Interfaces
1 interface between chains.
- A–B · 908 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4YBR · Structure of Mycobacterium tuberculosis NadD in complex with NADP, P21212 · the same entry in another collection · chain A against A, TM-score 1.00
- P9WJJ5 · AlphaFold monomer V2.0 prediction for probable nicotinate-nucleotide adenylyltransferase… · a predicted model of the same protein · chain A against A, TM-score 0.92
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 P9WJJ5
- Elsewhere: RCSB PDB 4YBR · PDBe 4YBR · UniProt P9WJJ5
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