MolNFT v1 · #173508 · protein
Complement inhibitor CIRPA3 from rhipicephalus pulchellus
7B28: “Complement inhibitor CIRPA3 from rhipicephalus pulchellus”. X-ray diffraction, 1 ligand (SO4), 12 pockets (best druggability 0.79). MolNFT v1 #173508 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7B28
- Type
- protein
- Length
- 1,217 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CIRPA3
- Ligands
- SO4
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | CIRPA3 | protein | 155 | 10% helix, 44% strand | — |
| A, B, D, E, H | CIRPA3 | protein | 151 | 11% helix, 44% strand | — |
| C | CIRPA3 | protein | 153 | 10% helix, 41% strand | — |
| G | CIRPA3 | protein | 154 | 10% helix, 42% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains F, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 828 | 0.79 | 0.82 | 106 | empty |
| 2 | 940 | 0.75 | 0.78 | 92 | empty |
| 3 | 491 | 0.69 | 0.80 | 79 | empty |
| 4 | 575 | 0.64 | 0.76 | 46 | empty |
| 5 | 233 | 0.57 | 0.79 | 31 | empty |
Interfaces
13 interfaces between chains.
- F–G · 671 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 641 Ų buried · 12 hydrogen bonds · protein-protein
- E–H · 638 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 564 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 520 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 7B28 · Complement inhibitor CirpA3 from Rhipicephalus pulchellus · the same entry in another collection · chain F against F, 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
- Elsewhere: RCSB PDB 7B28 · PDBe 7B28
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