Research workbench
Binding of NB113 camelid antibody fragment with the binary DHFR:FOLATE complex
Analyse Binding of NB113 camelid antibody fragment with the binary DHFR:FOLATE complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EJ1
- Type
- protein
- Length
- 570 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrofolate reductase; NB113 camelid antibody fragment
- EC
- 1.5.1.3
- UniProt
- P0ABQ4
- Ligands
- FOL, PO4
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydrofolate reductase (EC 1.5.1.3) | protein | 159 | 26% helix, 30% strand | P0ABQ4 |
| C, D | NB113 camelid antibody fragment | protein | 126 | 10% helix, 51% strand | — |
Ligands and binding sites
- FOL · Folic acid · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 6 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 428 | 0.72 | 0.82 | 48 | FOL, PO4 |
| 2 | 322 | 0.67 | 0.82 | 40 | FOL |
| 3 | 797 | 0.65 | 0.74 | 65 | empty |
| 4 | 102 | 0.42 | 0.77 | 20 | empty |
| 5 | 103 | 0.41 | 0.77 | 20 | empty |
Interfaces
4 interfaces between chains.
- B–C · 580 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 540 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 400 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 388 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4EJ1 · Binding of Nb113 camelid antibody fragment with the binary DHFR:folate complex · the same entry in another collection · chain A against A, TM-score 1.00
- P0ABQ4 · AlphaFold monomer V2.0 prediction for dihydrofolate reductase (P0ABQ4) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P0ABQ4
- Elsewhere: RCSB PDB 4EJ1 · PDBe 4EJ1 · UniProt P0ABQ4
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