Research workbench
Type IV coupling complex (T4CC) from L. pneumophila.
Analyse Type IV coupling complex (T4CC) from L. pneumophila. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SZ9
- Type
- protein
- Length
- 1,290 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Icmo (dotl); Icmp (dotm); Icmj (dotn); Dotz; Doty
- UniProt
- Q5ZYC6, Q5ZYC7, Q5ZYB7, Q5ZV91, Q5ZYR7
- Ligands
- ZN
- Pockets
- 17 · best druggability 0.78
Structure
electron microscopy · 5 distinct chains · 52% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Icmo (dotl) | protein | 473 | 42% helix, 11% strand | Q5ZYC6 |
| B | Icmp (dotm) | protein | 259 | 47% helix, 3% strand | Q5ZYC7 |
| C | Icmj (dotn) | protein | 202 | 48% helix, 8% strand | Q5ZYB7 |
| D | Dotz | protein | 283 | 72% helix, 0% strand | Q5ZV91 |
| E | Doty | protein | 73 | 63% helix, 0% strand | Q5ZYR7 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1049 | 0.78 | 0.80 | 88 | empty |
| 2 | 665 | 0.69 | 0.77 | 58 | empty |
| 3 | 285 | 0.59 | 0.78 | 47 | empty |
| 4 | 114 | 0.56 | 0.84 | 30 | empty |
| 5 | 306 | 0.55 | 0.76 | 37 | empty |
Interfaces
9 interfaces between chains.
- A–B · 3381 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 1818 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1598 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1475 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 683 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6SZ9 · Type IV Coupling Complex (T4CC) from L. pneumophila. · 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 Q5ZYC6
- Every structure of UniProt Q5ZYC7
- Every structure of UniProt Q5ZYB7
- Every structure of UniProt Q5ZV91
- Every structure of UniProt Q5ZYR7
- Elsewhere: RCSB PDB 6SZ9 · PDBe 6SZ9 · UniProt Q5ZYC6 · UniProt Q5ZYC7 · UniProt Q5ZYB7 · UniProt Q5ZV91 · UniProt Q5ZYR7
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