MolNFT v1 · #112624 · protein
Cdii from escherichia COLI EC869 in complex with a macrocyclic peptide
4ZQW · Immunity protein cdii-O11: “Cdii from escherichia COLI EC869 in complex with a macrocyclic peptide”. X-ray diffraction, 1 ligand (CL), 2 pockets (best druggability 0.75). MolNFT v1 #112624 on GenesisL1: 3D structure, binding sites…
- PDB
- 4ZQW
- Type
- protein
- Length
- 360 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunity protein cdii-O11; Macrocyclic peptide
- UniProt
- B3BM81
- Ligands
- CL
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | Immunity protein cdii-O11 | protein | 167 | 37% helix, 31% strand | B3BM81 |
| A, C | Macrocyclic peptide | protein | 13 | 0% helix, 46% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains B, A, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 534 | 0.75 | 0.83 | 43 | CL |
| 2 | 62 | 0.42 | 0.81 | 17 | empty |
Interfaces
5 interfaces between chains.
- D–C · 822 Ų buried · 23 hydrogen bonds · protein-protein
- B–A · 817 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 254 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 236 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 235 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 4ZQW · CdiI from Escherichia coli EC869 in complex with a macrocyclic peptide · the same entry in another collection · chain B against B, TM-score 1.00
- B3BM81 · AlphaFold monomer V2.0 prediction for immunity protein cdii-O11 (B3BM81) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 B3BM81
- Elsewhere: RCSB PDB 4ZQW · PDBe 4ZQW · UniProt B3BM81
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