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The crystal structure of holo CALE6, a methionine gamma lyase from micromonospora echinospora
Analyse The crystal structure of holo CALE6, a methionine gamma lyase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4U1T
- Type
- protein
- Length
- 2,939 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CALE6
- EC
- 4.4.1.11
- UniProt
- Q8KNG3
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 7 distinct chains · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CALE6 (EC 4.4.1.11) | protein | 368 | 33% helix, 17% strand | Q8KNG3 |
| B, F | CALE6 (EC 4.4.1.11) | protein | 377 | 39% helix, 17% strand | Q8KNG3 |
| C | CALE6 (EC 4.4.1.11) | protein | 362 | 37% helix, 17% strand | Q8KNG3 |
| D | CALE6 (EC 4.4.1.11) | protein | 361 | 37% helix, 17% strand | Q8KNG3 |
| E | CALE6 (EC 4.4.1.11) | protein | 366 | 36% helix, 17% strand | Q8KNG3 |
| G | CALE6 (EC 4.4.1.11) | protein | 363 | 37% helix, 17% strand | Q8KNG3 |
| H | CALE6 (EC 4.4.1.11) | protein | 365 | 38% helix, 17% strand | Q8KNG3 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D, E, 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 | 917 | 0.85 | 0.87 | 81 | empty |
| 2 | 378 | 0.78 | 0.87 | 36 | empty |
| 3 | 80 | 0.77 | 0.98 | 17 | empty |
| 4 | 394 | 0.77 | 0.86 | 37 | empty |
| 5 | 82 | 0.77 | 0.97 | 18 | empty |
Interfaces
15 interfaces between chains.
- E–F · 1998 Ų buried · 44 hydrogen bonds · protein-protein
- G–H · 1983 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 1979 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 1975 Ų buried · 41 hydrogen bonds · protein-protein
- B–C · 1747 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (cofactor).
Compared structures
- 4U1T · The crystal structure of holo CalE6, a methionine gamma lyase from Micromonospora… · 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 4U1T · PDBe 4U1T · UniProt Q8KNG3
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