MolNFT v1 · #117282 · protein
Crystal structure of cdia-CT/CDII complex from Y. kristensenii 33638
5E3E · Cdii immunity protein: “Crystal structure of cdia-CT/CDII complex from Y. kristensenii 33638”. X-ray diffraction, 1 ligand (NA), 10 pockets (best druggability 0.76). MolNFT v1 #117282 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5E3E
- Type
- protein
- Length
- 633 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cdii immunity protein; Large exoprotein involved in heme utilization or adhesion
- UniProt
- C4TSS4, C4TSS5
- Ligands
- NA
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Cdii immunity protein | protein | 99 | 70% helix, 1% strand | C4TSS4 |
| B, F | Large exoprotein involved in heme utilization or adhesion | protein | 114 | 32% helix, 33% strand | C4TSS5 |
| C | Cdii immunity protein | protein | 94 | 70% helix, 1% strand | C4TSS4 |
| D | Large exoprotein involved in heme utilization or adhesion | protein | 113 | 32% helix, 34% strand | C4TSS5 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 310 | 0.76 | 0.88 | 46 | empty |
| 2 | 262 | 0.56 | 0.77 | 36 | empty |
| 3 | 255 | 0.55 | 0.77 | 54 | empty |
| 4 | 164 | 0.54 | 0.80 | 32 | empty |
| 5 | 122 | 0.42 | 0.76 | 17 | empty |
Interfaces
11 interfaces between chains.
- C–D · 1140 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 1117 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1075 Ų buried · 22 hydrogen bonds · protein-protein
- B–E · 329 Ų buried · 4 hydrogen bonds · protein-protein
- B–F · 314 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 modified (engineered).
Compared structures
- 5E3E · Crystal structure of CdiA-CT/CdiI complex from Y. kristensenii 33638 · 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 C4TSS4
- Every structure of UniProt C4TSS5
- Elsewhere: RCSB PDB 5E3E · PDBe 5E3E · UniProt C4TSS4 · UniProt C4TSS5
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