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The crystal structure of cystathione gamma lyase (CALE6) from micromonospora echinospora
Analyse The crystal structure of cystathione gamma lyase (CALE6) from micromonospora… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q31
- Type
- protein
- Length
- 3,018 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cystathione gamma lyase 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 | Cystathione gamma lyase CALE6 | protein | 376 | 38% helix, 16% strand | Q8KNG3 |
| B, G, H | Cystathione gamma lyase CALE6 | protein | 378 | 36% helix, 16% strand | Q8KNG3 |
| C | Cystathione gamma lyase CALE6 | protein | 379 | 36% helix, 17% strand | Q8KNG3 |
| E | Cystathione gamma lyase CALE6 | protein | 376 | 36% helix, 16% strand | Q8KNG3 |
| F | Cystathione gamma lyase CALE6 | protein | 377 | 39% helix, 17% 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 · 5 copies · chains A, C, F, G, H
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 | 1136 | 0.83 | 0.84 | 111 | CL, GOL |
| 2 | 374 | 0.77 | 0.87 | 38 | empty |
| 3 | 80 | 0.77 | 0.97 | 20 | empty |
| 4 | 81 | 0.77 | 0.97 | 17 | empty |
| 5 | 344 | 0.76 | 0.87 | 38 | empty |
Interfaces
15 interfaces between chains.
- C–D · 2133 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 2059 Ų buried · 43 hydrogen bonds · protein-protein
- G–H · 2038 Ų buried · 37 hydrogen bonds · protein-protein
- E–F · 1976 Ų buried · 40 hydrogen bonds · protein-protein
- F–G · 1612 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered, cofactor).
Compared structures
- 4Q31 · The crystal structure of cystathione gamma lyase (CalE6) 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 4Q31 · PDBe 4Q31 · UniProt Q8KNG3
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