8ZCA | pdb_00008zca

Crystal structure of human CD47 ECD bound to Fab of Hu1C8

PDB DOI: https://doi.org/10.2210/pdb8ZCA/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2024-04-29 Released: 2025-05-07
Deposition Author(s): Chen, Z., Ding, J.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 ?
R-Value Free:
0.266 (Depositor), 0.265 (DCC)
R-Value Work:
0.215 (Depositor), 0.215 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

The humanized antibody Hu1C8 binds to a distinct epitope of CD47 in a novel metal ion-dependent manner to induce low RBC toxicity and effective antitumour activity

Lu, X., Sun, B.

To be published.

Macromolecule Content

Total Structure Weight: 126.12 kDa
Atom Count: 8,567
Modelled Residue Count: 1,091
Deposited Residue Count: 1,148
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1C8 Fab light chain	A, C [auth B]	218	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
1C8 Fab heavy chain	B [auth D], D [auth C]	225	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Leukocyte surface antigen CD47	E, F	131	Homo sapiens	Mutation(s): 0 Gene Names: CD47, MER6
UniProt & NIH Common Fund Data Resources
Find proteins for Q08722 (Homo sapiens) Explore Q08722 Go to UniProtKB: Q08722
PHAROS: Q08722 GTEx: ENSG00000196776
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q08722
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain E Focus chain F	Go to GlyGen: Q08722-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain K [auth E] SDF format, chain L [auth E] SDF format, chain M [auth F] SDF format, chain N [auth F] MOL2 format, chain K [auth E] MOL2 format, chain L [auth E] MOL2 format, chain M [auth F] MOL2 format, chain N [auth F] mmCIF format, chain K [auth E] mmCIF format, chain L [auth E] mmCIF format, chain M [auth F] mmCIF format, chain N [auth F]	K [auth E], L [auth E], M [auth F], N [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain K [auth E] Focus chain L [auth E] Focus chain M [auth F] Focus chain N [auth F] Interactions & Density Focus chain K [auth E] Focus chain L [auth E] Focus chain M [auth F] Focus chain N [auth F]
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain J [auth C] MOL2 format, chain H [auth D] MOL2 format, chain J [auth C] mmCIF format, chain H [auth D] mmCIF format, chain J [auth C]	H [auth D], J [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth D] Focus chain J [auth C] Interactions & Density Focus chain H [auth D] Focus chain J [auth C]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B]	G [auth A], I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Interactions & Density Focus chain G [auth A] Focus chain I [auth B]