MolNFT v1 · #121753 · protein
Contact-dependent inhibition system from escherichia COLI NC101 - ternary CDIA/CDII/EF-tu complex (trypsin-modified)
5I4R · Contact-dependent inhibitor a: “Contact-dependent inhibition system from escherichia COLI NC101 - ternary CDIA/CDII/EF-tu complex…”. X-ray diffraction, 1 ligand (GDP), 12 pockets (best druggability 0.76). MolNFT v1 #121753 on…
- PDB
- 5I4R
- Type
- protein
- Length
- 1,123 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Contact-dependent inhibitor a; Elongation factor tu; Contact-dependent inhibitor I
- UniProt
- A7ZSL4
- Ligands
- GDP
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 7 distinct chains · 38% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Contact-dependent inhibitor a | protein | 87 | 21% helix, 39% strand | — |
| C | Elongation factor tu | protein | 34 | 47% helix, 24% strand | A7ZSL4 |
| D, H | Elongation factor tu | protein | 335 | 21% helix, 40% strand | A7ZSL4 |
| B | Contact-dependent inhibitor I | protein | 107 | 76% helix, 0% strand | — |
| E | Contact-dependent inhibitor a | protein | 86 | 21% helix, 40% strand | — |
| G | Elongation factor tu | protein | 33 | 45% helix, 24% strand | A7ZSL4 |
| F | Contact-dependent inhibitor I | protein | 106 | 76% helix, 0% strand | — |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains C, D, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 997 | 0.76 | 0.78 | 107 | empty |
| 2 | 292 | 0.60 | 0.79 | 35 | empty |
| 3 | 202 | 0.60 | 0.81 | 30 | empty |
| 4 | 134 | 0.58 | 0.84 | 20 | empty |
| 5 | 124 | 0.57 | 0.84 | 18 | empty |
Interfaces
11 interfaces between chains.
- C–D · 1973 Ų buried · 25 hydrogen bonds · protein-protein
- G–H · 1951 Ų buried · 28 hydrogen bonds · protein-protein
- B–F · 1324 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 1025 Ų buried · 12 hydrogen bonds · protein-protein
- E–H · 979 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 5I4R · Contact-dependent inhibition system from Escherichia coli NC101 - ternary CdiA/CdiI/EF-Tu… · the same entry in another collection · chain G against G, TM-score 1.00
- A7ZSL4 · AlphaFold monomer V2.0 prediction for elongation factor tu 1 (A7ZSL4) · a predicted model of the same protein · chain C against A, TM-score 0.90
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 A7ZSL4
- Elsewhere: RCSB PDB 5I4R · PDBe 5I4R · UniProt A7ZSL4
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