Research workbench
Free structure of an anti-methotrexate CDR1-4 graft vhh antibody
Analyse Free structure of an anti-methotrexate CDR1-4 graft vhh antibody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QXW
- Type
- protein
- Length
- 614 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-methotrexate CDR1-4 graft vhh
- Ligands
- NA, SO4
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Anti-methotrexate CDR1-4 graft vhh | protein | 124 | 12% helix, 48% strand | — |
| C | Anti-methotrexate CDR1-4 graft vhh | protein | 119 | 5% helix, 49% strand | — |
| D | Anti-methotrexate CDR1-4 graft vhh | protein | 123 | 8% helix, 48% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 340 | 0.59 | 0.77 | 31 | empty |
| 2 | 327 | 0.57 | 0.76 | 36 | empty |
| 3 | 300 | 0.56 | 0.77 | 33 | SO4 |
| 4 | 97 | 0.36 | 0.75 | 14 | empty |
Interfaces
4 interfaces between chains.
- A–C · 420 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 415 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 377 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 290 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 3QXW · Free structure of an anti-methotrexate CDR1-4 Graft VHH Antibody · the same entry in another collection · chain A against A, 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 3QXW · PDBe 3QXW
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