Research workbench
VH1-69 germline antibody predicted from CR6261
Analyse VH1-69 germline antibody predicted from CR6261 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WKZ
- Type
- protein
- Length
- 433 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin heavy variable 1-69D,IGG H chain; Lambda-chain (aa -20 to 215)
- UniProt
- A0A0B4J2H0, S6BAM6, A2NUT2
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Immunoglobulin heavy variable 1-69D,IGG H chain | protein | 221 | 10% helix, 52% strand | A0A0B4J2H0, S6BAM6 |
| L | Lambda-chain (aa -20 to 215) | protein | 212 | 8% helix, 51% strand | A2NUT2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.46 | 0.73 | 34 | empty |
| 2 | 106 | 0.41 | 0.77 | 23 | empty |
| 3 | 85 | 0.33 | 0.74 | 21 | empty |
| 4 | 61 | 0.30 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- H–L · 1681 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5WKZ · VH1-69 germline antibody predicted from CR6261 · the same entry in another collection · chain H against H, TM-score 1.00
- 4NUG · Crystal structure of HIV-1 broadly neutralizing antibody PGT151 · an experimental structure of the same protein · chain H against H, TM-score 0.90
- 4NUG · Crystal structure of HIV-1 broadly neutralizing antibody PGT151 · an experimental structure of the same protein · chain H against H, TM-score 0.90
- 5CBA · 3B4 in complex with CXCL13 - 3B4-CXCL13 · an experimental structure of the same protein · chain H against C, TM-score 0.52
- 5CBA · 3B4 in complex with CXCL13 - 3B4-CXCL13 · an experimental structure of the same protein · chain H against A, TM-score 0.52
- 5C6W · anti-CXCL13 scFv - E10 · an experimental structure of the same protein · chain H against J, TM-score 0.52
- 5C6W · Anti-CXCL13 scfv - E10 · an experimental structure of the same protein · chain H against J, TM-score 0.52
- 5C2B · anti-CXCL13 parental scFv - 3B4 · an experimental structure of the same protein · chain H against H, TM-score 0.52
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 S6BAM6
- Every structure of UniProt A2NUT2
- Elsewhere: RCSB PDB 5WKZ · PDBe 5WKZ · UniProt A0A0B4J2H0 · AlphaFold DB A0A0B4J2H0 · UniProt S6BAM6 · AlphaFold DB S6BAM6 · UniProt A2NUT2 · AlphaFold DB A2NUT2
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