Download MendeleyPD-L1 de novo binder
Zhao, L.To be published.
8ZNL | pdb_00008znl
PD-L1 de novo designed binder with picomolar binding affinity
- PDB DOI: https://doi.org/10.2210/pdb8ZNL/pdb
- Classification: DE NOVO PROTEIN
- Organism(s): Escherichia coli, Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2024-05-27 Released: 2025-06-04
- Funding Organization(s): National Natural Science Foundation of China (NSFC)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.77 ?
- R-Value Free: 0.275 (Depositor), 0.273 (DCC)
- R-Value Work: 0.201 (Depositor), 0.199 (DCC)
- R-Value Observed: 0.204 (Depositor)
Starting Model: in silico
View more details
wwPDB Validation 3D Report Full Report
This is version 1.0 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| PD-L1 de novo binder | 58 | Escherichia coli | 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: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Programmed cell death 1 ligand 1 | 114 | Homo sapiens | Mutation(s): 0 Gene Names: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9NZQ7 (Homo sapiens) Explore Q9NZQ7 Go to UniProtKB: Q9NZQ7 | |||||
PHAROS: Q9NZQ7 GTEx: ENSG00000120217 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9NZQ7 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| BR Query on BR | I [auth A], J [auth D], K [auth E], L [auth H] | BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.77 ?
- R-Value Free: 0.275 (Depositor), 0.273 (DCC)
- R-Value Work: 0.201 (Depositor), 0.199 (DCC)
- R-Value Observed: 0.204 (Depositor)
Space Group: P 1
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 44.872 | ¦Á = 92.52 |
| b = 58.956 | ¦Â = 90.02 |
| c = 63.299 | ¦Ă = 94.8 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2025-06-04 Deposition Author(s): Zhao, L.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Natural Science Foundation of China (NSFC) | China | 8227130865 |
Revision History (Full details and data files)
- Version 1.0: 2025-06-04
Type: Initial release
