Download MendeleyVenom protection by antibody from a snakebite hyperimmune subject
Glanville, J., Andrade, J., Bellin, M., Kim, S., Pletnev, S., Tsao, D., Verardi, R., Bedi, R., Friede, T., Tully, E., Zhang, B., Bylund, T., Liu, T., Kwong, P.D.To be published.
8D9Z
Crystal structure of Cobra alpha-neurotoxin in complex with Centi-3FTX-D09 antibody
- PDB DOI: https://doi.org/10.2210/pdb8D9Z/pdb
- Classification: IMMUNE SYSTEM,ANTITOXIN/TOXIN
- Organism(s): Homo sapiens, Naja nivea
- Expression System: Homo sapiens
- Mutation(s): No
- Deposited: 2022-06-12 Released: 2023-06-14
- Funding Organization(s): Bill & Melinda Gates Foundation, National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.198
- R-Value Work: 0.165
- R-Value Observed: 0.165
wwPDB Validation 3D Report Full Report
This is version 1.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Centi-3FTX-D09 Fab light chain | 214 | Homo sapiens | Mutation(s): 0 |  | |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
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 |
| Centi-3FTX-D09 Fab heavy chain | 237 | Homo sapiens | Mutation(s): 0 |  | |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Long neurotoxin 1 | C [auth D] | 77 | Naja nivea | Mutation(s): 0 |  |
UniProt | |||||
Find proteins for P01390 (Naja nivea) Explore P01390 Go to UniProtKB: P01390 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P01390 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GOL Query on GOL | D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| ACT Query on ACT | N [auth D] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.198
- R-Value Work: 0.165
- R-Value Observed: 0.165
- Space Group: P 32 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 61.285 | α = 90 |
| b = 61.285 | β = 90 |
| c = 260.046 | γ = 120 |
| Software Name | Purpose |
|---|---|
| SCALEPACK | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data reduction |
| BALBES | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2023-06-14 Deposition Author(s): Pletnev, S., Verardi, R., Tully, E.S., Glanville, J., Kwong, P.D.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Bill & Melinda Gates Foundation | United States | -- |
| National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | -- |
Revision History (Full details and data files)
- Version 1.0: 2023-06-14
Type: Initial release
