MolNFT v1 · #158854 · protein
The structure of egtb (cabther)
6O6M: “The structure of egtb (cabther)”. X-ray diffraction, 1 ligand (FE), 17 pockets (best druggability 0.87). MolNFT v1 #158854 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6O6M
- Type
- protein
- Length
- 1,623 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Egtb (cabther)
- UniProt
- G2LET6
- Ligands
- FE
- Pockets
- 17 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Egtb (cabther) | protein | 407 | 42% helix, 14% strand | G2LET6 |
| B | Egtb (cabther) | protein | 406 | 41% helix, 14% strand | G2LET6 |
| C | Egtb (cabther) | protein | 405 | 41% helix, 13% strand | G2LET6 |
| D | Egtb (cabther) | protein | 405 | 42% helix, 14% strand | G2LET6 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1072 | 0.87 | 0.88 | 102 | empty |
| 2 | 1043 | 0.87 | 0.88 | 98 | empty |
| 3 | 360 | 0.79 | 0.88 | 45 | FE |
| 4 | 454 | 0.78 | 0.86 | 52 | FE |
| 5 | 377 | 0.78 | 0.88 | 44 | FE, GOL |
Interfaces
4 interfaces between chains.
- B–D · 1328 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1313 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1125 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1112 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6O6M · The Structure of EgtB (Cabther) · 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 G2LET6
- Elsewhere: RCSB PDB 6O6M · PDBe 6O6M · UniProt G2LET6
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