Research workbench
Crystal structure of the dioxygenase cctet from coprinopsis cinereain in complex with MN(II) and N-oxalylglycine
Analyse Crystal structure of the dioxygenase cctet from coprinopsis cinereain in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VPN
- Type
- protein
- Length
- 1,388 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cctet molecule
- UniProt
- A8P1J0
- Ligands
- OGA, MN
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cctet molecule | protein | 347 | 41% helix, 19% strand | A8P1J0 |
| B | Cctet molecule | protein | 351 | 39% helix, 19% strand | A8P1J0 |
| C | Cctet molecule | protein | 356 | 40% helix, 18% strand | A8P1J0 |
| D | Cctet molecule | protein | 334 | 39% helix, 18% strand | A8P1J0 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · chains A
- MN · Manganese (II) 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
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 828 | 0.82 | 0.84 | 87 | empty |
| 2 | 1062 | 0.81 | 0.82 | 100 | empty |
| 3 | 492 | 0.70 | 0.80 | 51 | MN, OGA |
| 4 | 261 | 0.67 | 0.83 | 28 | MN |
| 5 | 308 | 0.66 | 0.82 | 35 | MN |
Interfaces
5 interfaces between chains.
- C–D · 647 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 559 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 502 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 459 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 253 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7VPN · Crystal Structure of the dioxygenase CcTet from Coprinopsis cinereain in complex with… · 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 A8P1J0
- Elsewhere: RCSB PDB 7VPN · PDBe 7VPN · UniProt A8P1J0
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