Research workbench
Ensemble refinement of cystathione gamma lyase (CALE6) D7G from micromonospora echinospora
Analyse Ensemble refinement of cystathione gamma lyase (CALE6) D7G from micromonospora… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XQ2
- Type
- protein
- Length
- 3,018 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CALE6
- UniProt
- Q8KNG3
- Ligands
- CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | CALE6 | protein | 376 | 36% helix, 16% strand | Q8KNG3 |
| B, G, H | CALE6 | protein | 378 | 37% helix, 16% strand | Q8KNG3 |
| C | CALE6 | protein | 379 | 37% helix, 17% strand | Q8KNG3 |
| E | CALE6 | protein | 376 | 36% helix, 16% strand | Q8KNG3 |
| F | CALE6 | protein | 377 | 39% helix, 15% strand | Q8KNG3 |
Ligands and binding sites
- CL · Chloride ion · ion · 12 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 28 copies · chains A, C, B, D, E, F, G, H
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 8 copies · chains A, B, C, D, E, F, G, H
- FMT · Formic acid · additive · 3 copies · chains C, F, G
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 | 1092 | 0.83 | 0.84 | 104 | GOL |
| 2 | 364 | 0.77 | 0.87 | 37 | empty |
| 3 | 83 | 0.77 | 0.97 | 19 | empty |
| 4 | 78 | 0.76 | 0.97 | 17 | empty |
| 5 | 336 | 0.76 | 0.87 | 36 | empty |
Interfaces
15 interfaces between chains.
- C–D · 2174 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 2107 Ų buried · 41 hydrogen bonds · protein-protein
- G–H · 2093 Ų buried · 43 hydrogen bonds · protein-protein
- E–F · 2044 Ų buried · 35 hydrogen bonds · protein-protein
- A–D · 1631 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered, cofactor).
Compared structures
- 4XQ2 · Ensemble refinement of cystathione gamma lyase (CalE6) D7G from Micromonospora echinospora · 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 Q8KNG3
- Elsewhere: RCSB PDB 4XQ2 · PDBe 4XQ2 · UniProt Q8KNG3
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