MolNFT v1 · #129188 · protein
Crystal structure of acpa E4 in complex with cii-C-48-cit
5OCY · Acpa E4 Fab fragment - heavy chain: “Crystal structure of acpa E4 in complex with cii-C-48-cit”. X-ray diffraction, 1 ligand (CIR), 4 pockets (best druggability 0.67). MolNFT v1 #129188 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5OCY
- Type
- protein
- Length
- 433 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acpa E4 Fab fragment - heavy chain; Acpa E4 Fab fragment - light chain; Cii-C-48-cit
- Ligands
- CIR
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Acpa E4 Fab fragment - heavy chain | protein | 211 | 3% helix, 55% strand | — |
| L | Acpa E4 Fab fragment - light chain | protein | 214 | 8% helix, 50% strand | — |
| C | Cii-C-48-cit | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- CIR · Citrulline · ligand · chains H, L, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 642 | 0.67 | 0.76 | 55 | empty |
| 2 | 99 | 0.42 | 0.78 | 23 | empty |
| 3 | 75 | 0.32 | 0.75 | 19 | empty |
| 4 | 60 | 0.28 | 0.73 | 15 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1838 Ų buried · 17 hydrogen bonds · protein-protein
- H–C · 302 Ų buried · 4 hydrogen bonds · protein-protein
- L–C · 240 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 covalent, 1 modified (disulfide, covalent ligand, cyclization).
Compared structures
- 5OCY · Crystal structure of ACPA E4 in complex with CII-C-48-CIT · the same entry in another collection · chain H against H, 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 5OCY · PDBe 5OCY
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