Research workbench
Complex of inlc of listeria monocytogenes and human tuba C-terminal SH3 domain
Analyse Complex of inlc of listeria monocytogenes and human tuba C-terminal SH3 domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CC4
- Type
- protein
- Length
- 990 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inlc protein; Dynamin-binding protein
- UniProt
- P71451, Q6XZF7
- Ligands
- CL, SO4, PO4
- Pockets
- 12 · best druggability 0.62
Structure
x-ray diffraction · 5 distinct chains · 13% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inlc protein | protein | 265 | 15% helix, 29% strand | P71451 |
| B, F | Dynamin-binding protein | protein | 67 | 4% helix, 43% strand | Q6XZF7 |
| C | Inlc protein | protein | 265 | 14% helix, 30% strand | P71451 |
| D | Dynamin-binding protein | protein | 63 | 5% helix, 41% strand | Q6XZF7 |
| E | Inlc protein | protein | 263 | 15% helix, 28% strand | P71451 |
Ligands and binding sites
- CL · Chloride ion · ion · 6 copies · chains A, C, D, F
- SO4 · Sulfate ion · ion · 2 copies · chains A, C, D
- PO4 · Phosphate ion · ion · 2 copies · chains E
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D, E, F
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 525 | 0.62 | 0.75 | 62 | GOL |
| 2 | 312 | 0.57 | 0.77 | 42 | PE4, SO4, CL, GOL |
| 3 | 236 | 0.53 | 0.77 | 33 | empty |
| 4 | 214 | 0.51 | 0.77 | 33 | empty |
| 5 | 176 | 0.49 | 0.77 | 27 | empty |
Interfaces
5 interfaces between chains.
- E–F · 869 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 860 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 611 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 477 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 335 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (oxidation).
Compared structures
- 4CC4 · Complex of InlC of Listeria monocytogenes and human Tuba C-terminal SH3 domain · the same entry in another collection · chain F against F, TM-score 1.00
- P71451 · AlphaFold monomer V2.0 prediction for internalin C (P71451) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q6XZF7 · AlphaFold monomer V2.0 prediction for dynamin-binding protein (Q6XZF7) · a predicted model of the same protein · chain F against A, TM-score 0.89
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 P71451
- Every structure of UniProt Q6XZF7
- Elsewhere: RCSB PDB 4CC4 · PDBe 4CC4 · UniProt P71451 · UniProt Q6XZF7
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