Research workbench
Crystal structure of the AGCARB2-C2 complex with homoorientin
Analyse Crystal structure of the AGCARB2-C2 complex with homoorientin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DNN
- Type
- protein
- Length
- 934 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AP_ENDONUC_2 domain-containing protein; AGCARC2
- UniProt
- H0QPL9, H0QPL8
- Ligands
- H9R, MN, IOD
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, P | AP_ENDONUC_2 domain-containing protein | protein | 336 | 51% helix, 15% strand | H0QPL9 |
| B, Q | AGCARC2 | protein | 131 | 11% helix, 51% strand | H0QPL8 |
Ligands and binding sites
- H9R · 2-[3,4-bis(oxidanyl)phenyl]-6-[(2S,3R,4R,5S,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-5,7-bis(oxidanyl)chromen-4-one · ligand · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, P
- IOD · Iodide ion · ion · 2 copies · chains A, B, P, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 490 | 0.76 | 0.84 | 50 | H9R, IOD |
| 2 | 585 | 0.74 | 0.81 | 50 | IOD |
| 3 | 148 | 0.45 | 0.77 | 34 | empty |
| 4 | 109 | 0.41 | 0.77 | 21 | empty |
| 5 | 52 | 0.40 | 0.81 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1642 Ų buried · 28 hydrogen bonds · protein-protein
- P–Q · 1340 Ų buried · 25 hydrogen bonds · protein-protein
- A–P · 396 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7DNN · Crystal structure of the AgCarB2-C2 complex with homoorientin · 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 H0QPL9
- Every structure of UniProt H0QPL8
- Elsewhere: RCSB PDB 7DNN · PDBe 7DNN · UniProt H0QPL9 · UniProt H0QPL8
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