MolNFT v1 · #174886 · protein
The structure of product-bound cntl, an aminobutyrate transferase in staphylopine biosynthesis
7C9M · D-histidine 2-aminobutanoyltransferase: “The structure of product-bound cntl, an aminobutyrate transferase in staphylopine biosynthesis”. X-ray diffraction, 2 ligands (FN6, MTA), 15 pockets (best druggability 0.77). MolNFT v1…
- PDB
- 7C9M
- Type
- protein
- Length
- 1,029 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-histidine 2-aminobutanoyltransferase
- EC
- 2.5.1.152
- UniProt
- A0A0H3JXA8
- Ligands
- FN6, MTA
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | D-histidine 2-aminobutanoyltransferase (EC 2.5.1.152) | protein | 259 | 48% helix, 15% strand | A0A0H3JXA8 |
| C | D-histidine 2-aminobutanoyltransferase (EC 2.5.1.152) | protein | 260 | 52% helix, 15% strand | A0A0H3JXA8 |
| D | D-histidine 2-aminobutanoyltransferase (EC 2.5.1.152) | protein | 251 | 50% helix, 16% strand | A0A0H3JXA8 |
Ligands and binding sites
- FN6 · (2S)-2-azanyl-4-[[(2R)-3-(1H-imidazol-4-yl)-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]butanoic acid · ligand · 4 copies · chains A, B, C, D
- MTA · 5'-deoxy-5'-methylthioadenosine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 374 | 0.77 | 0.87 | 46 | FN6, MTA |
| 2 | 405 | 0.77 | 0.86 | 52 | FN6, MTA |
| 3 | 337 | 0.76 | 0.87 | 47 | FN6, MTA |
| 4 | 370 | 0.72 | 0.84 | 52 | FN6, MTA |
| 5 | 150 | 0.68 | 0.88 | 28 | empty |
Interfaces
4 interfaces between chains.
- B–D · 625 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 514 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 252 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 69 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7C9M · The structure of product-bound CntL, an aminobutyrate transferase in staphylopine… · 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 A0A0H3JXA8
- Elsewhere: RCSB PDB 7C9M · PDBe 7C9M · UniProt A0A0H3JXA8
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