Research workbench
Native structure of egtb from chloracidobacterium thermophilum, a type II sulfoxide synthase
Analyse Native structure of egtb from chloracidobacterium thermophilum, a type II… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QKI
- Type
- protein
- Length
- 1,572 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- G2LET6
- Ligands
- FE
- Pockets
- 14 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 395 | 42% helix, 13% strand | G2LET6 |
| B | Uncharacterized protein | protein | 392 | 41% helix, 13% strand | G2LET6 |
| C | Uncharacterized protein | protein | 393 | 42% helix, 13% strand | G2LET6 |
| D | Uncharacterized protein | protein | 392 | 41% helix, 13% strand | G2LET6 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1198 | 0.86 | 0.87 | 86 | empty |
| 2 | 1191 | 0.86 | 0.87 | 84 | empty |
| 3 | 1133 | 0.79 | 0.81 | 110 | FE |
| 4 | 844 | 0.75 | 0.79 | 89 | FE |
| 5 | 615 | 0.71 | 0.79 | 45 | FE |
Interfaces
4 interfaces between chains.
- A–B · 1295 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1292 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1071 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1066 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6QKI · Native structure of EgtB from Chloracidobacterium thermophilum, a type II sulfoxide… · 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 6QKI · PDBe 6QKI · UniProt G2LET6
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