MolNFT v1 · #115011 · protein
Anti-CXCL13 scfv - E10
5C6W · Protein IGHV1-69-2,IG lambda chain V-II region nig-84: “Anti-CXCL13 scfv - E10”. X-ray diffraction, 2 ligands (CL, SO4), 5 pockets (best druggability 0.82). MolNFT v1 #115011 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5C6W
- Type
- protein
- Length
- 475 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein IGHV1-69-2,IG lambda chain V-II region nig-84
- UniProt
- A0A0B4J2H0, P04209
- Ligands
- CL, SO4
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Protein IGHV1-69-2,IG lambda chain V-II region nig-84 | protein | 237 | 4% helix, 51% strand | A0A0B4J2H0, P04209 |
| J | Protein IGHV1-69-2,IG lambda chain V-II region nig-84 | protein | 238 | 4% helix, 51% strand | A0A0B4J2H0, P04209 |
Ligands and binding sites
- CL · Chloride ion · ion · 6 copies · chains H, J
- SO4 · Sulfate ion · ion · 5 copies · chains H, J
- EDO · 1,2-ethanediol · additive · 29 copies · chains H, J
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains H, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1039 | 0.82 | 0.84 | 127 | EDO |
| 2 | 50 | 0.51 | 0.88 | 21 | EDO |
| 3 | 96 | 0.48 | 0.81 | 21 | EDO |
| 4 | 90 | 0.42 | 0.79 | 21 | EDO |
| 5 | 64 | 0.26 | 0.72 | 16 | empty |
Interfaces
1 interface between chains.
- H–J · 1038 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5C6W · anti-CXCL13 scFv - E10 · 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 0.49
- 5WKZ · VH1-69 germline antibody predicted from CR6261 · a predicted model of the same protein · chain H against H, TM-score 0.49
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 P04209
- Elsewhere: RCSB PDB 5C6W · PDBe 5C6W · UniProt A0A0B4J2H0 · UniProt P04209
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