MolNFT v1 · #107186 · protein
The crystal structure of apo CALE6, a methionine gamma lyase from micromonospora echinospora
4U2H: “The crystal structure of apo CALE6, a methionine gamma lyase from micromonospora echinospora”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.85). MolNFT v1 #107186 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4U2H
- Type
- protein
- Length
- 2,906 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 · 8 distinct chains · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CALE6 (EC 4.4.1.11) | protein | 362 | 37% helix, 17% strand | Q8KNG3 |
| B | CALE6 (EC 4.4.1.11) | protein | 365 | 38% helix, 17% strand | Q8KNG3 |
| C | CALE6 (EC 4.4.1.11) | protein | 360 | 36% helix, 17% strand | Q8KNG3 |
| D | CALE6 (EC 4.4.1.11) | protein | 366 | 38% helix, 17% strand | Q8KNG3 |
| E | CALE6 (EC 4.4.1.11) | protein | 366 | 36% helix, 17% strand | Q8KNG3 |
| F | CALE6 (EC 4.4.1.11) | protein | 362 | 37% helix, 17% strand | Q8KNG3 |
| G | CALE6 (EC 4.4.1.11) | protein | 361 | 35% helix, 18% strand | Q8KNG3 |
| H | CALE6 (EC 4.4.1.11) | protein | 364 | 36% helix, 17% strand | Q8KNG3 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 16 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 | 971 | 0.85 | 0.86 | 82 | empty |
| 2 | 103 | 0.78 | 0.98 | 38 | empty |
| 3 | 354 | 0.78 | 0.88 | 35 | empty |
| 4 | 80 | 0.77 | 0.97 | 18 | empty |
| 5 | 82 | 0.77 | 0.97 | 20 | empty |
Interfaces
15 interfaces between chains.
- C–D · 1976 Ų buried · 36 hydrogen bonds · protein-protein
- G–H · 1907 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 1905 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 1886 Ų buried · 33 hydrogen bonds · protein-protein
- F–G · 1684 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 4U2H · The crystal structure of apo 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 4U2H · PDBe 4U2H · UniProt Q8KNG3
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