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Structure of the pore C-terminal domain, a protein of T9SS from porphyromonas gingivalis
Analyse Structure of the pore C-terminal domain, a protein of T9SS from porphyromonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TOP
- Type
- protein
- Length
- 604 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ompa family protein
- UniProt
- T2NEY1
- Ligands
- MLD, NA
- Pockets
- 11 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ompa family protein | protein | 154 | 40% helix, 16% strand | T2NEY1 |
| B, C, D | Ompa family protein | protein | 150 | 41% helix, 17% strand | T2NEY1 |
Ligands and binding sites
- MLD · Glcnac(beta1-4)-murnac(1,6-anhydro)-L-ala-gamma-D-glu-meso-A2PM-D-ala · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 83 | 0.72 | 0.95 | 31 | empty |
| 2 | 56 | 0.69 | 0.97 | 19 | empty |
| 3 | 412 | 0.69 | 0.81 | 63 | empty |
| 4 | 405 | 0.67 | 0.80 | 69 | empty |
| 5 | 51 | 0.67 | 0.96 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1287 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1276 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1040 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 987 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 85 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6TOP · Structure of the PorE C-terminal domain, a protein of T9SS from Porphyromonas gingivalis · 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 T2NEY1
- Elsewhere: RCSB PDB 6TOP · PDBe 6TOP · UniProt T2NEY1
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