MolNFT v1 · #38915 · protein
Crystal structure of the colicin I receptor cir from E.COLI in complex with receptor binding domain of colicin ia.
2HDI: “Crystal structure of the colicin I receptor cir from E.COLI in complex with receptor binding domain of…”. X-ray diffraction, 6 pockets (best druggability 0.86). MolNFT v1 #38915 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2HDI
- Type
- protein
- Length
- 701 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Colicin I receptor; Colicin-ia
- UniProt
- P17315, P06716
- Pockets
- 6 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Colicin I receptor | protein | 598 | 7% helix, 60% strand | P17315 |
| B | Colicin-ia | protein | 103 | 47% helix, 21% strand | P06716 |
Ligands and binding sites
- LDA · Lauryl dimethylamine-N-oxide · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1187 | 0.86 | 0.87 | 116 | empty |
| 2 | 600 | 0.76 | 0.82 | 58 | empty |
| 3 | 94 | 0.75 | 0.97 | 28 | empty |
| 4 | 280 | 0.71 | 0.86 | 38 | empty |
| 5 | 218 | 0.55 | 0.78 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1016 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2HDI · Crystal structure of the Colicin I receptor Cir from E.coli in complex with receptor… · the same entry in another collection · chain A against A, TM-score 1.00
- P17315 · AlphaFold monomer V2.0 prediction for colicin I receptor (P17315) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P06716 · AlphaFold monomer V2.0 prediction for colicin-ia (P06716) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P17315
- Every structure of UniProt P06716
- Elsewhere: RCSB PDB 2HDI · PDBe 2HDI · UniProt P17315 · UniProt P06716
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