9IYK

Crystal structure of hSOD1 in C121 space group

PDB DOI: https://doi.org/10.2210/pdb9IYK/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-07-30 Released: 2024-08-14
Deposition Author(s): Yapici, I., DeMirci, H.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free: 0.263
R-Value Work: 0.198
R-Value Observed: 0.201

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The New Crystal Form of hSOD1

Yapici, I., DeMirci, H.

To be published.

Macromolecule Content

Total Structure Weight: 196.44 kDa
Atom Count: 14,379
Modelled Residue Count: 1,840
Deposited Residue Count: 1,872
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Cu-Zn]	A B [auth C] C [auth K] D [auth F] E A, B [auth C], C [auth K], D [auth F], E, F [auth D], G [auth B], H [auth G], I, J [auth L], K [auth J], L [auth H]	156	Homo sapiens	Mutation(s): 0 Gene Names: SOD1 EC: 1.15.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00441 (Homo sapiens) Explore P00441 Go to UniProtKB: P00441
PHAROS: P00441 GTEx: ENSG00000142168
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00441
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 (Subject of Investigation/LOI) Query on SO4 Download Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain MA [auth I] SDF format, chain Q [auth A] SDF format, chain V [auth C] MOL2 format, chain CA [auth E] MOL2 format, chain MA [auth I] MOL2 format, chain Q [auth A] MOL2 format, chain V [auth C] mmCIF format, chain CA [auth E] mmCIF format, chain MA [auth I] mmCIF format, chain Q [auth A] mmCIF format, chain V [auth C]	CA [auth E], MA [auth I], Q [auth A], V [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain CA [auth E] Focus chain MA [auth I] Focus chain Q [auth A] Focus chain V [auth C] Interactions & Density Focus chain CA [auth E] Focus chain MA [auth I] Focus chain Q [auth A] Focus chain V [auth C]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain EA [auth D] SDF format, chain GA [auth B] SDF format, chain JA [auth G] SDF format, chain LA [auth I] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain OA [auth L] SDF format, chain QA [auth J] SDF format, chain SA [auth H] SDF format, chain T [auth C] SDF format, chain X [auth K] SDF format, chain Z [auth F] MOL2 format, chain BA [auth E] MOL2 format, chain EA [auth D] MOL2 format, chain GA [auth B] MOL2 format, chain JA [auth G] MOL2 format, chain LA [auth I] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth L] MOL2 format, chain QA [auth J] MOL2 format, chain SA [auth H] MOL2 format, chain T [auth C] MOL2 format, chain X [auth K] MOL2 format, chain Z [auth F] mmCIF format, chain BA [auth E] mmCIF format, chain EA [auth D] mmCIF format, chain GA [auth B] mmCIF format, chain JA [auth G] mmCIF format, chain LA [auth I] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth L] mmCIF format, chain QA [auth J] mmCIF format, chain SA [auth H] mmCIF format, chain T [auth C] mmCIF format, chain X [auth K] mmCIF format, chain Z [auth F]	BA [auth E] EA [auth D] GA [auth B] JA [auth G] LA [auth I] BA [auth E], EA [auth D], GA [auth B], JA [auth G], LA [auth I], N [auth A], O [auth A], OA [auth L], QA [auth J], SA [auth H], T [auth C], X [auth K], Z [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain EA [auth D] Focus chain GA [auth B] Focus chain JA [auth G] Focus chain LA [auth I] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth L] Focus chain QA [auth J] Focus chain SA [auth H] Focus chain T [auth C] Focus chain X [auth K] Focus chain Z [auth F] Interactions & Density Focus chain BA [auth E] Focus chain EA [auth D] Focus chain GA [auth B] Focus chain JA [auth G] Focus chain LA [auth I] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth L] Focus chain QA [auth J] Focus chain SA [auth H] Focus chain T [auth C] Focus chain X [auth K] Focus chain Z [auth F]
CU (Subject of Investigation/LOI) Query on CU Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain DA [auth D] SDF format, chain FA [auth B] SDF format, chain IA [auth G] SDF format, chain KA [auth I] SDF format, chain M [auth A] SDF format, chain NA [auth L] SDF format, chain PA [auth J] SDF format, chain RA [auth H] SDF format, chain S [auth C] SDF format, chain W [auth K] SDF format, chain Y [auth F] MOL2 format, chain AA [auth E] MOL2 format, chain DA [auth D] MOL2 format, chain FA [auth B] MOL2 format, chain IA [auth G] MOL2 format, chain KA [auth I] MOL2 format, chain M [auth A] MOL2 format, chain NA [auth L] MOL2 format, chain PA [auth J] MOL2 format, chain RA [auth H] MOL2 format, chain S [auth C] MOL2 format, chain W [auth K] MOL2 format, chain Y [auth F] mmCIF format, chain AA [auth E] mmCIF format, chain DA [auth D] mmCIF format, chain FA [auth B] mmCIF format, chain IA [auth G] mmCIF format, chain KA [auth I] mmCIF format, chain M [auth A] mmCIF format, chain NA [auth L] mmCIF format, chain PA [auth J] mmCIF format, chain RA [auth H] mmCIF format, chain S [auth C] mmCIF format, chain W [auth K] mmCIF format, chain Y [auth F]	AA [auth E] DA [auth D] FA [auth B] IA [auth G] KA [auth I] AA [auth E], DA [auth D], FA [auth B], IA [auth G], KA [auth I], M [auth A], NA [auth L], PA [auth J], RA [auth H], S [auth C], W [auth K], Y [auth F]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain DA [auth D] Focus chain FA [auth B] Focus chain IA [auth G] Focus chain KA [auth I] Focus chain M [auth A] Focus chain NA [auth L] Focus chain PA [auth J] Focus chain RA [auth H] Focus chain S [auth C] Focus chain W [auth K] Focus chain Y [auth F] Interactions & Density Focus chain AA [auth E] Focus chain DA [auth D] Focus chain FA [auth B] Focus chain IA [auth G] Focus chain KA [auth I] Focus chain M [auth A] Focus chain NA [auth L] Focus chain PA [auth J] Focus chain RA [auth H] Focus chain S [auth C] Focus chain W [auth K] Focus chain Y [auth F]
ACT (Subject of Investigation/LOI) Query on ACT Download Ideal Coordinates CCD File SDF format, chain HA [auth B] SDF format, chain P [auth A] SDF format, chain R [auth C] SDF format, chain U [auth C] MOL2 format, chain HA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain R [auth C] MOL2 format, chain U [auth C] mmCIF format, chain HA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain R [auth C] mmCIF format, chain U [auth C]	HA [auth B], P [auth A], R [auth C], U [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain HA [auth B] Focus chain P [auth A] Focus chain R [auth C] Focus chain U [auth C] Interactions & Density Focus chain HA [auth B] Focus chain P [auth A] Focus chain R [auth C] Focus chain U [auth C]