Research workbench
Lysinoalanine cross-linked flge dimer from treponema denticola
Analyse Lysinoalanine cross-linked flge dimer from treponema denticola in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NDX
- Type
- protein
- Length
- 762 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Flagellar hook protein flge
- UniProt
- Q9RQB6
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Flagellar hook protein flge | protein | 218 | 6% helix, 46% strand | Q9RQB6 |
| A | Flagellar hook protein flge | protein | 201 | 6% helix, 32% strand | Q9RQB6 |
| C | Flagellar hook protein flge | protein | 171 | 2% helix, 40% strand | Q9RQB6 |
| D | Flagellar hook protein flge | protein | 172 | 3% helix, 40% strand | Q9RQB6 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 343 | 0.80 | 0.89 | 49 | empty |
| 2 | 123 | 0.42 | 0.76 | 22 | empty |
| 3 | 64 | 0.33 | 0.76 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 895 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 782 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 85 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 d-amino (D-amino acid).
Compared structures
- 6NDX · Lysinoalanine cross-linked FlgE dimer from Treponema denticola · the same entry in another collection · chain B against B, 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 Q9RQB6
- Elsewhere: RCSB PDB 6NDX · PDBe 6NDX · UniProt Q9RQB6
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