MolNFT v1 · #114859 · protein
Anti-CXCL13 parental scfv - 3B4
5C2B · Scfv 3B4: “Anti-CXCL13 parental scfv - 3B4”. X-ray diffraction, 1 ligand (CL), 3 pockets (best druggability 0.46). MolNFT v1 #114859 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5C2B
- Type
- protein
- Length
- 241 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Scfv 3B4
- UniProt
- A0A0B4J2H0, A0A5C2GBJ8
- Ligands
- CL
- Pockets
- 3 · best druggability 0.46
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Scfv 3B4 | protein | 241 | 5% helix, 51% strand | A0A0B4J2H0, A0A5C2GBJ8 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.46 | 0.79 | 20 | empty |
| 2 | 76 | 0.37 | 0.78 | 21 | empty |
| 3 | 93 | 0.34 | 0.74 | 18 | empty |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5C2B · anti-CXCL13 parental scFv - 3B4 · the same entry in another collection · chain H against H, TM-score 1.00
- 5WKZ · VH1-69 germline antibody predicted from CR6261 · a predicted model of the same protein · chain H against H, TM-score 0.48
- 5WKZ · VH1-69 germline antibody predicted from CR6261 · a predicted model of the same protein · chain H against H, TM-score 0.48
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 A0A0B4J2H0
- Every structure of UniProt A0A5C2GBJ8
- Elsewhere: RCSB PDB 5C2B · PDBe 5C2B · UniProt A0A0B4J2H0 · UniProt A0A5C2GBJ8
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