MolNFT v1 · #176466 · protein
Crystal structure of the AGCARB2-C2 complex
7DNM · AP_ENDONUC_2 domain-containing protein: “Crystal structure of the AGCARB2-C2 complex”. X-ray diffraction, 2 ligands (MN, IOD), 8 pockets (best druggability 0.75). MolNFT v1 #176466 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7DNM
- Type
- protein
- Length
- 939 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
- MN, IOD
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, P | AP_ENDONUC_2 domain-containing protein | protein | 336 | 52% helix, 15% strand | H0QPL9 |
| B | AGCARC2 | protein | 134 | 9% helix, 50% strand | H0QPL8 |
| Q | AGCARC2 | protein | 133 | 9% helix, 51% strand | H0QPL8 |
Ligands and binding sites
- 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
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 621 | 0.75 | 0.82 | 56 | IOD |
| 2 | 593 | 0.75 | 0.82 | 66 | IOD |
| 3 | 215 | 0.54 | 0.78 | 41 | empty |
| 4 | 109 | 0.41 | 0.77 | 29 | empty |
| 5 | 71 | 0.34 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1585 Ų buried · 28 hydrogen bonds · protein-protein
- P–Q · 1343 Ų buried · 26 hydrogen bonds · protein-protein
- A–P · 386 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7DNM · Crystal structure of the AgCarB2-C2 complex · 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 7DNM · PDBe 7DNM · UniProt H0QPL9 · UniProt H0QPL8
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