MolNFT v1 · #122764 · protein
Protein-protein interaction
5IZ8 · Adenomatous polyposis COLI protein: “Protein-protein interaction”. X-ray diffraction, 2 ligands (ACE, NH2), 4 pockets (best druggability 0.72). MolNFT v1 #122764 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5IZ8
- Type
- protein
- Length
- 679 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenomatous polyposis COLI protein; ACE-ala-gly-glu-ala-leu-ala-asp-NH2
- UniProt
- P25054
- Ligands
- ACE, NH2
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenomatous polyposis COLI protein | protein | 343 | 73% helix, 0% strand | P25054 |
| B | Adenomatous polyposis COLI protein | protein | 322 | 74% helix, 0% strand | P25054 |
| C, D | ACE-ala-gly-glu-ala-leu-ala-asp-NH2 | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, C, B, D
- NH2 · Amino group · ion · 2 copies · chains B, C, D
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1049 | 0.72 | 0.76 | 82 | ACE |
| 2 | 471 | 0.69 | 0.80 | 46 | empty |
| 3 | 91 | 0.41 | 0.77 | 16 | empty |
| 4 | 101 | 0.39 | 0.76 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–B · 716 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 577 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 564 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 219 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5IZ8 · Protein-protein interaction · 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 P25054
- Elsewhere: RCSB PDB 5IZ8 · PDBe 5IZ8 · UniProt P25054
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