Research workbench
Structure of mycobacterium tuberculosis nadd in complex with inhibitor [(1~{R},2~{R},5~{S})-5-methyl-2-propan-2-yl-cyclohexyl] 2-[3-methyl- 2-(PHENOXYMETHYL)BENZIMIDAZOL-1-YL]ETHANOATE
Analyse Structure of mycobacterium tuberculosis nadd in complex with inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BUV
- Type
- protein
- Length
- 380 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinate mononucleotide adenylyltransferase nadd
- EC
- 2.7.7.18
- UniProt
- P9WJJ5
- Ligands
- E9A, NA, CL
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicotinate mononucleotide adenylyltransferase nadd (EC 2.7.7.18) | protein | 189 | 44% helix, 19% strand | P9WJJ5 |
| B | Nicotinate mononucleotide adenylyltransferase nadd (EC 2.7.7.18) | protein | 191 | 46% helix, 20% strand | P9WJJ5 |
Ligands and binding sites
- E9A · [(1~{R},2~{R},5~{S})-5-methyl-2-propan-2-yl-cyclohexyl] 2-[3-methyl-2-(phenoxymethyl)benzimidazol-1-yl]ethanoate · ligand · chains B
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · 5 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 | 457 | 0.71 | 0.81 | 45 | empty |
| 2 | 391 | 0.68 | 0.81 | 40 | CL |
| 3 | 83 | 0.49 | 0.83 | 19 | empty |
| 4 | 160 | 0.44 | 0.75 | 33 | empty |
| 5 | 85 | 0.38 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 982 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6BUV · Structure of Mycobacterium tuberculosis NadD in complex with inhibitor… · 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 0.95
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 6BUV · PDBe 6BUV · UniProt P9WJJ5
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