MolNFT v1 · #59814 · protein
High resolution crystal structure of argos bound to the EGF domain of spitz
3C9A · Protein giant-lens: “High resolution crystal structure of argos bound to the EGF domain of spitz”. X-ray diffraction, 1 ligand (BR), 10 pockets (best druggability 0.81). MolNFT v1 #59814 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3C9A
- Type
- protein
- Length
- 511 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein giant-lens; Protein spitz
- UniProt
- Q00805, Q01083
- Ligands
- BR
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein giant-lens | protein | 208 | 1% helix, 47% strand | Q00805 |
| B | Protein giant-lens | protein | 207 | 3% helix, 48% strand | Q00805 |
| C, D | Protein spitz | protein | 48 | 13% helix, 35% strand | Q01083 |
Ligands and binding sites
- BR · Bromide ion · ion · 18 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 382 | 0.81 | 0.90 | 49 | empty |
| 2 | 429 | 0.75 | 0.84 | 62 | BR |
| 3 | 128 | 0.48 | 0.79 | 22 | empty |
| 4 | 121 | 0.47 | 0.79 | 21 | empty |
| 5 | 155 | 0.44 | 0.75 | 21 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1414 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 1333 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 540 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 433 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 disulfide (disulfide).
Compared structures
- 3C9A · High Resolution Crystal Structure of Argos bound to the EGF domain of Spitz · the same entry in another collection · chain A against A, TM-score 1.00
- Q00805 · AlphaFold monomer V2.0 prediction for protein giant-lens (Q00805) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q01083 · AlphaFold monomer V2.0 prediction for protein spitz (Q01083) · a predicted model of the same protein · chain C against A, TM-score 0.95
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 Q00805
- Every structure of UniProt Q01083
- Elsewhere: RCSB PDB 3C9A · PDBe 3C9A · UniProt Q00805 · UniProt Q01083
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