MolNFT v1 · #117709 · protein
The crystal structure of semet-ct
5EGF · Tqaa: “The crystal structure of semet-ct”. X-ray diffraction, 20 pockets (best druggability 0.85). MolNFT v1 #117709 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5EGF
- Type
- protein
- Length
- 1,771 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tqaa
- UniProt
- F1CWE4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Tqaa | protein | 442 | 33% helix, 24% strand | F1CWE4 |
| B | Tqaa | protein | 443 | 33% helix, 24% strand | F1CWE4 |
| C | Tqaa | protein | 444 | 34% helix, 23% strand | F1CWE4 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 35 copies · chains A, B, C, D
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 767 | 0.85 | 0.87 | 57 | EDO, C8E |
| 2 | 708 | 0.84 | 0.87 | 59 | C8E, EDO |
| 3 | 443 | 0.74 | 0.83 | 44 | EDO |
| 4 | 636 | 0.73 | 0.80 | 60 | EDO |
| 5 | 372 | 0.72 | 0.83 | 45 | EDO |
Interfaces
4 interfaces between chains.
- B–C · 1160 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1040 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 940 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 924 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 5EGF · The crystal structure of SeMet-CT · 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 F1CWE4
- Elsewhere: RCSB PDB 5EGF · PDBe 5EGF · UniProt F1CWE4
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