MolNFT v1 · #137470 · protein
Crystal structure of der F 1 complexed with Fab 4C1
5VPL · Der F 1 variant: “Crystal structure of der F 1 complexed with Fab 4C1”. X-ray diffraction, 2 ligands (NAG, CA), 5 pockets (best druggability 0.62). MolNFT v1 #137470 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5VPL
- Type
- protein
- Length
- 650 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Der F 1 variant; 4C1 - light chain; 4C1 - heavy chain
- UniProt
- I2CMD3, Q7TS98
- Ligands
- NAG, CA
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Der F 1 variant | protein | 223 | 28% helix, 24% strand | I2CMD3 |
| C | 4C1 - light chain | protein | 211 | 6% helix, 52% strand | Q7TS98 |
| D | 4C1 - heavy chain | protein | 216 | 7% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- CA · Calcium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 626 | 0.62 | 0.74 | 61 | empty |
| 2 | 267 | 0.60 | 0.79 | 40 | EDO |
| 3 | 97 | 0.35 | 0.74 | 20 | empty |
| 4 | 61 | 0.33 | 0.76 | 15 | empty |
| 5 | 80 | 0.30 | 0.73 | 15 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2006 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 616 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 227 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5VPL · Crystal structure of der F 1 complexed with Fab 4C1 · 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
- Every structure of UniProt I2CMD3
- Every structure of UniProt Q7TS98
- Elsewhere: RCSB PDB 5VPL · PDBe 5VPL · UniProt I2CMD3 · UniProt Q7TS98
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