Research workbench
Structure of an anti-methotrexate CDR1-4 graft vhh antibody in complex with methotrexate
Analyse Structure of an anti-methotrexate CDR1-4 graft vhh antibody in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QXV
- Type
- protein
- Length
- 606 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-methotrexate CDR1-4 graft vhh
- Ligands
- MTX, SO4
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Anti-methotrexate CDR1-4 graft vhh | protein | 123 | 2% helix, 47% strand | — |
| D | Anti-methotrexate CDR1-4 graft vhh | protein | 124 | 7% helix, 48% strand | — |
| E | Anti-methotrexate CDR1-4 graft vhh | protein | 113 | 5% helix, 43% strand | — |
Ligands and binding sites
- MTX · Methotrexate · ligand · 5 copies · chains A, B, C, D, E
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.69 | 0.80 | 46 | MTX |
| 2 | 129 | 0.62 | 0.86 | 22 | MTX |
| 3 | 108 | 0.62 | 0.87 | 22 | MTX |
| 4 | 115 | 0.59 | 0.86 | 22 | MTX |
| 5 | 472 | 0.59 | 0.74 | 53 | empty |
Interfaces
6 interfaces between chains.
- C–D · 405 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 397 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 394 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 305 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 255 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 3QXV · Structure of an Anti-Methotrexate CDR1-4 Graft VHH Antibody in Complex with Methotrexate · the same entry in another collection · chain B against B, 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 3QXV · PDBe 3QXV
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