9X9P | pdb_00009x9p

crystal structure of Cd(II)Ca(II)Mg(II)-bound human calprotectin

PDB DOI: https://doi.org/10.2210/pdb9X9P/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-10-21 Released: 2026-10-28
Deposition Author(s): Tao, X.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.219 (Depositor), 0.227 (DCC)
R-Value Work:
0.167 (Depositor), 0.177 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

crystal structure of Cd(II)Ca(II)Mg(II)-bound human calprotectin

Tao, X.

To be published.

Macromolecule Content

Total Structure Weight: 99.57 kDa
Atom Count: 7,537
Modeled Residue Count: 792
Deposited Residue Count: 832
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein S100-A9	A, C, E, G	114	Homo sapiens	Mutation(s): 0 Gene Names: S100A9, CAGB, CFAG, MRP14
UniProt & NIH Common Fund Data Resources
Find proteins for P06702 (Homo sapiens) Explore P06702 Go to UniProtKB: P06702
PHAROS: P06702 GTEx: ENSG00000163220
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06702
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein S100-A8	B, D, F, H	94	Homo sapiens	Mutation(s): 0 Gene Names: S100A8, CAGA, CFAG, MRP8
UniProt & NIH Common Fund Data Resources
Find proteins for P05109 (Homo sapiens) Explore P05109 Go to UniProtKB: P05109
PHAROS: P05109 GTEx: ENSG00000143546
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05109
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain UA [auth G] MOL2 format, chain K [auth A] MOL2 format, chain UA [auth G] mmCIF format, chain K [auth A] mmCIF format, chain UA [auth G]	K [auth A], UA [auth G]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain UA [auth G] Interactions & Density Focus chain K [auth A] Focus chain UA [auth G]
CD (Subject of Investigation/LOI) Query on CD Download:Ideal Coordinates CCD File SDF format, chain LA [auth E] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain VA [auth G] SDF format, chain W [auth C] SDF format, chain X [auth C] MOL2 format, chain LA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain VA [auth G] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] mmCIF format, chain LA [auth E] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain VA [auth G] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C]	LA [auth E] M [auth A] N [auth A] VA [auth G] W [auth C] LA [auth E], M [auth A], N [auth A], VA [auth G], W [auth C], X [auth C]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain LA [auth E] Focus chain M [auth A] Focus chain N [auth A] Focus chain VA [auth G] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain LA [auth E] Focus chain M [auth A] Focus chain N [auth A] Focus chain VA [auth G] Focus chain W [auth C] Focus chain X [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain FA [auth E] SDF format, chain L [auth A] SDF format, chain R [auth B] SDF format, chain TA [auth G] SDF format, chain V [auth C] MOL2 format, chain FA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain R [auth B] MOL2 format, chain TA [auth G] MOL2 format, chain V [auth C] mmCIF format, chain FA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain R [auth B] mmCIF format, chain TA [auth G] mmCIF format, chain V [auth C]	FA [auth E], L [auth A], R [auth B], TA [auth G], V [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain FA [auth E] Focus chain L [auth A] Focus chain R [auth B] Focus chain TA [auth G] Focus chain V [auth C] Interactions & Density Focus chain FA [auth E] Focus chain L [auth A] Focus chain R [auth B] Focus chain TA [auth G] Focus chain V [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain IA [auth E] SDF format, chain JA [auth E] SDF format, chain KA [auth E] SDF format, chain SA [auth G] SDF format, chain U [auth C] SDF format, chain ZA [auth H] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain IA [auth E] MOL2 format, chain JA [auth E] MOL2 format, chain KA [auth E] MOL2 format, chain SA [auth G] MOL2 format, chain U [auth C] MOL2 format, chain ZA [auth H] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain IA [auth E] mmCIF format, chain JA [auth E] mmCIF format, chain KA [auth E] mmCIF format, chain SA [auth G] mmCIF format, chain U [auth C] mmCIF format, chain ZA [auth H]	BA [auth D] CA [auth D] DA [auth D] IA [auth E] JA [auth E] BA [auth D], CA [auth D], DA [auth D], IA [auth E], JA [auth E], KA [auth E], SA [auth G], U [auth C], ZA [auth H]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain SA [auth G] Focus chain U [auth C] Focus chain ZA [auth H] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain SA [auth G] Focus chain U [auth C] Focus chain ZA [auth H]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain GA [auth E] SDF format, chain HA [auth E] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain NA [auth F] SDF format, chain OA [auth F] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain QA [auth G] SDF format, chain RA [auth G] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain XA [auth H] SDF format, chain YA [auth H] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain HA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain NA [auth F] MOL2 format, chain OA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth G] MOL2 format, chain RA [auth G] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain XA [auth H] MOL2 format, chain YA [auth H] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain GA [auth E] mmCIF format, chain HA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain NA [auth F] mmCIF format, chain OA [auth F] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth G] mmCIF format, chain RA [auth G] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain XA [auth H] mmCIF format, chain YA [auth H] mmCIF format, chain Z [auth D]	AA [auth D] GA [auth E] HA [auth E] I [auth A] J [auth A] AA [auth D], GA [auth E], HA [auth E], I [auth A], J [auth A], NA [auth F], OA [auth F], P [auth B], Q [auth B], QA [auth G], RA [auth G], S [auth C], T [auth C], XA [auth H], YA [auth H], Z [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain I [auth A] Focus chain J [auth A] Focus chain NA [auth F] Focus chain OA [auth F] Focus chain P [auth B] Focus chain Q [auth B] Focus chain QA [auth G] Focus chain RA [auth G] Focus chain S [auth C] Focus chain T [auth C] Focus chain XA [auth H] Focus chain YA [auth H] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain I [auth A] Focus chain J [auth A] Focus chain NA [auth F] Focus chain OA [auth F] Focus chain P [auth B] Focus chain Q [auth B] Focus chain QA [auth G] Focus chain RA [auth G] Focus chain S [auth C] Focus chain T [auth C] Focus chain XA [auth H] Focus chain YA [auth H] Focus chain Z [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain MA [auth E] SDF format, chain O [auth A] SDF format, chain Y [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain MA [auth E] MOL2 format, chain O [auth A] MOL2 format, chain Y [auth C] mmCIF format, chain EA [auth D] mmCIF format, chain MA [auth E] mmCIF format, chain O [auth A] mmCIF format, chain Y [auth C]	EA [auth D], MA [auth E], O [auth A], Y [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain EA [auth D] Focus chain MA [auth E] Focus chain O [auth A] Focus chain Y [auth C] Interactions & Density Focus chain EA [auth D] Focus chain MA [auth E] Focus chain O [auth A] Focus chain Y [auth C]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain PA [auth F] SDF format, chain WA [auth G] MOL2 format, chain PA [auth F] MOL2 format, chain WA [auth G] mmCIF format, chain PA [auth F] mmCIF format, chain WA [auth G]	PA [auth F], WA [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain PA [auth F] Focus chain WA [auth G] Interactions & Density Focus chain PA [auth F] Focus chain WA [auth G]