MolNFT v1 · #166882 · protein
Structure of salmonella typhi ttsa
6V40 · PG_BINDING_3 domain-containing protein: “Structure of salmonella typhi ttsa”. X-ray diffraction, 1 ligand (API), 7 pockets (best druggability 0.77). MolNFT v1 #166882 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6V40
- Type
- protein
- Length
- 764 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PG_BINDING_3 domain-containing protein
- UniProt
- Q8Z6A5
- Ligands
- API
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 63% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PG_BINDING_3 domain-containing protein | protein | 193 | 63% helix, 3% strand | Q8Z6A5 |
| B | PG_BINDING_3 domain-containing protein | protein | 191 | 63% helix, 3% strand | Q8Z6A5 |
| C, D | PG_BINDING_3 domain-containing protein | protein | 190 | 63% helix, 2% strand | Q8Z6A5 |
Ligands and binding sites
- API · 2,6-diaminopimelic acid · ligand · 4 copies · chains A, B, C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1043 | 0.77 | 0.79 | 72 | empty |
| 2 | 626 | 0.74 | 0.81 | 67 | TRS |
| 3 | 144 | 0.46 | 0.77 | 29 | empty |
| 4 | 140 | 0.42 | 0.75 | 21 | empty |
| 5 | 69 | 0.36 | 0.77 | 15 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1751 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1744 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 476 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 257 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 99 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6V40 · Structure of Salmonella Typhi TtsA · 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 Q8Z6A5
- Elsewhere: RCSB PDB 6V40 · PDBe 6V40 · UniProt Q8Z6A5
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