Research workbench
Crystal structure of the soluble domain of trwg type IV secretion machinery from bartonella grahamii
Analyse Crystal structure of the soluble domain of trwg type IV secretion machinery… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NHF
- Type
- protein
- Length
- 851 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trwg protein
- UniProt
- C6AAT5
- Ligands
- CA
- Pockets
- 14 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trwg protein | protein | 144 | 35% helix, 32% strand | C6AAT5 |
| B | Trwg protein | protein | 138 | 36% helix, 33% strand | C6AAT5 |
| C, D, E | Trwg protein | protein | 142 | 34% helix, 32% strand | C6AAT5 |
| F | Trwg protein | protein | 143 | 35% helix, 32% strand | C6AAT5 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 672 | 0.74 | 0.80 | 58 | empty |
| 2 | 627 | 0.74 | 0.81 | 52 | empty |
| 3 | 673 | 0.74 | 0.80 | 58 | empty |
| 4 | 487 | 0.64 | 0.76 | 55 | empty |
| 5 | 56 | 0.54 | 0.87 | 12 | empty |
Interfaces
8 interfaces between chains.
- E–F · 774 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 744 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 737 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 633 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 126 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4NHF · Crystal structure of the soluble domain of TrwG Type IV secretion machinery from… · 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 C6AAT5
- Elsewhere: RCSB PDB 4NHF · PDBe 4NHF · UniProt C6AAT5
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