Research workbench
Crystal structure of the chts-DHFR F207A non-active site mutant
Analyse Crystal structure of the chts-DHFR F207A non-active site mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HJ3
- Type
- protein
- Length
- 2,033 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chain a, crystal structure of DHFR
- UniProt
- Q5CGA3
- Ligands
- MTX, NDP, UMP, CB3
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chain a, crystal structure of DHFR | protein | 508 | 29% helix, 25% strand | Q5CGA3 |
| B | Chain a, crystal structure of DHFR | protein | 510 | 30% helix, 26% strand | Q5CGA3 |
| C | Chain a, crystal structure of DHFR | protein | 510 | 28% helix, 24% strand | Q5CGA3 |
| D | Chain a, crystal structure of DHFR | protein | 505 | 29% helix, 24% strand | Q5CGA3 |
Ligands and binding sites
- MTX · Methotrexate · ligand · 4 copies · chains A, B, C, D
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 3 copies · chains A, B, C, D
- CB3 · 10-propargyl-5,8-dideazafolic acid · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 499 | 0.81 | 0.87 | 53 | UMP, CB3 |
| 2 | 457 | 0.79 | 0.87 | 42 | UMP, CB3 |
| 3 | 445 | 0.78 | 0.86 | 49 | UMP, CB3 |
| 4 | 372 | 0.76 | 0.86 | 40 | empty |
| 5 | 912 | 0.73 | 0.77 | 79 | empty |
Interfaces
3 interfaces between chains.
- C–D · 4326 Ų buried · 64 hydrogen bonds · protein-protein
- A–B · 4270 Ų buried · 62 hydrogen bonds · protein-protein
- B–C · 358 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3HJ3 · Crystal Structure of the ChTS-DHFR F207A Non-Active Site Mutant · 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
- Every structure of UniProt Q5CGA3
- Elsewhere: RCSB PDB 3HJ3 · PDBe 3HJ3 · UniProt Q5CGA3
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