MolNFT v1 · #127886 · protein
Structure of adenylation domain THR1 involved in the biosynthesis of 4-chlorothreonine in streptomyces SP.OH-5093, ligand bound structure
5N9X: “Structure of adenylation domain THR1 involved in the biosynthesis of 4-chlorothreonine in streptomyces…”. X-ray diffraction, 4 ligands (THR, ATP, 8QN), 9 pockets (best druggability 0.83). MolNFT v1 #127886 on GenesisL1: 3D…
- PDB
- 5N9X
- Type
- protein
- Length
- 975 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylation domain
- UniProt
- H6SG27
- Ligands
- THR, ATP, 8QN, MG
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenylation domain | protein | 489 | 34% helix, 27% strand | H6SG27 |
| B | Adenylation domain | protein | 486 | 32% helix, 28% strand | H6SG27 |
Ligands and binding sites
- THR · Threonine · ligand · chains A
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- 8QN · [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2~{S},3~{R})-2-azanyl-3-oxidanyl-butanoate · ligand · chains B
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1199 | 0.83 | 0.84 | 116 | 8QN |
| 2 | 959 | 0.80 | 0.82 | 91 | THR, ATP, MG |
| 3 | 414 | 0.73 | 0.83 | 52 | empty |
| 4 | 401 | 0.72 | 0.82 | 39 | empty |
| 5 | 188 | 0.46 | 0.75 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 695 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5N9X · Structure of adenylation domain THR1 involved in the biosynthesis of 4-chlorothreonine in… · 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 H6SG27
- Elsewhere: RCSB PDB 5N9X · PDBe 5N9X · UniProt H6SG27
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