5VPL
CRYSTAL STRUCTURE OF DER F 1 COMPLEXED WITH FAB 4C1
- PDB DOI: https://doi.org/10.2210/pdb5VPL/pdb
- Entry: 5VPL supersedes: 3RVV
- Classification: HYDROLASE/IMMUNE SYSTEM
- Organism(s): Dermatophagoides farinae, Mus musculus
- Expression System: Mus musculus
- Mutation(s): No
- Deposited: 2017-05-05 Released: 2017-05-24
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.194
- R-Value Work: 0.152
- R-Value Observed: 0.154
This is version 1.3 of the entry. See complete history.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Der f 1 variant | 223 | Dermatophagoides farinae | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for P16311 (Dermatophagoides farinae) Explore P16311 Go to UniProtKB: P16311 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P16311 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 4C1 - LIGHT CHAIN | B [auth C] | 213 | Mus musculus | Mutation(s): 0 |  |
UniProt | |||||
Find proteins for Q7TS98 (Mus musculus) Explore Q7TS98 Go to UniProtKB: Q7TS98 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q7TS98 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 4C1 - HEAVY CHAIN | C [auth D] | 255 | Mus musculus | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | D [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| EDO Query on EDO | F [auth A], G [auth A], H [auth C], I [auth C] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| CA Query on CA | E [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.194
- R-Value Work: 0.152
- R-Value Observed: 0.154
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 65.403 | α = 90 |
| b = 79.428 | β = 105.2 |
| c = 72.199 | γ = 90 |
| Software Name | Purpose |
|---|---|
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| HKL-3000 | phasing |
| MOLREP | phasing |
| REFMAC | refinement |
Entry History
Deposition Data
- Released Date: 2017-05-24 Deposition Author(s): Chruszcz, M., Vailes, L.D., Chapman, M.D., Pomes, A., Minor, W.
- This entry supersedes: 3RVV
Revision History (Full details and data files)
- Version 1.0: 2017-05-24
Type: Initial release - Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.2: 2022-04-13
Changes: Database references, Structure summary - Version 1.3: 2023-10-04
Changes: Data collection, Refinement description
