Research workbench
Crystal structure of GFP-lama-F98 - a GFP enhancer nanobody with cpdhfr insertion and tmp and NADPH
Analyse Crystal structure of GFP-lama-F98 - a GFP enhancer nanobody with cpdhfr… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RUL
- Type
- protein
- Length
- 276 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GFP-lama-F98 a GFP enhancer nanobody with cpdhfr insertion, dihydrofolate…
- EC
- 1.5.1.3
- UniProt
- P0ABQ4
- Ligands
- TOP, NDP
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GFP-lama-F98 a GFP enhancer nanobody with cpdhfr insertion, dihydrofolate REDUCTASE,GFP-lama-F98 a GFP enhancer nanobody with cpdhfr INSERTION,DIHYDROFOLATE REDUCTASE,DIHYDROFOLATE REDUCTASE,GFP- lama-F98 a GFP enhancer nanobody with cpdhfr INSERTION,DIHYDROFOLATE REDUCTASE,GFP-lama-F98 a GFP enhancer nanobody with cpdhfr insertion (EC 1.5.1.3) | protein | 276 | 18% helix, 40% strand | P0ABQ4 |
Ligands and binding sites
- TOP · Trimethoprim · ligand · chains A
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 482 | 0.71 | 0.81 | 52 | TOP, NDP |
| 2 | 59 | 0.27 | 0.73 | 13 | PGE |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6RUL · Crystal structure of GFP-LAMA-F98 - a GFP enhancer nanobody with cpDHFR insertion and TMP… · 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 0.50
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 6RUL · PDBe 6RUL · UniProt P0ABQ4
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