MolNFT v1 · #55270 · protein
Crystal structure of the oligomerisation domain of C4B-binding protein from gallus gallus
2YF2 · C4B binding protein: “Crystal structure of the oligomerisation domain of C4B-binding protein from gallus gallus”. X-ray diffraction, 4 pockets (best druggability 0.55). MolNFT v1 #55270 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2YF2
- Type
- protein
- Length
- 364 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C4B binding protein
- UniProt
- E1C2T5
- Pockets
- 4 · best druggability 0.55
Structure
x-ray diffraction · 7 distinct chains · 89% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C4B binding protein | protein | 57 | 91% helix, 0% strand | E1C2T5 |
| B | C4B binding protein | protein | 46 | 89% helix, 0% strand | E1C2T5 |
| C | C4B binding protein | protein | 58 | 90% helix, 0% strand | E1C2T5 |
| D | C4B binding protein | protein | 46 | 85% helix, 0% strand | E1C2T5 |
| E | C4B binding protein | protein | 55 | 91% helix, 0% strand | E1C2T5 |
| F | C4B binding protein | protein | 45 | 89% helix, 0% strand | E1C2T5 |
| G | C4B binding protein | protein | 57 | 89% helix, 0% strand | E1C2T5 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 19 copies · chains A, G, B, C, D, E, F
- ACT · Acetate ion · additive · 11 copies · chains A, F, G, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 327 | 0.55 | 0.75 | 35 | EDO |
| 2 | 366 | 0.53 | 0.73 | 36 | EDO, ACT |
| 3 | 53 | 0.48 | 0.85 | 11 | empty |
| 4 | 74 | 0.30 | 0.73 | 11 | empty |
Interfaces
14 interfaces between chains.
- B–C · 1127 Ų buried · 2 hydrogen bonds · protein-protein
- A–G · 1109 Ų buried · 3 hydrogen bonds · protein-protein
- F–G · 1099 Ų buried · 2 hydrogen bonds · protein-protein
- D–E · 1065 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 1006 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 2YF2 · Crystal structure of the oligomerisation domain of C4b-binding protein from Gallus gallus · 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 E1C2T5
- Elsewhere: RCSB PDB 2YF2 · PDBe 2YF2 · UniProt E1C2T5
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