8YD3 | pdb_00008yd3

Crystal structure of human Cu-Zn Superoxide Dismutase 1 in complex with 1,2,10-Decanetriol

PDB DOI: https://doi.org/10.2210/pdb8YD3/pdb

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

Deposited: 2024-02-19 Released: 2024-08-21
Deposition Author(s): Aouti, S., Padmanabhan, B.
Funding Organization(s): Indian Council of Medical Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free:
0.211 (Depositor), 0.210 (DCC)
R-Value Work:
0.179 (Depositor), 0.180 (DCC)
R-Value Observed:
0.181 (Depositor)

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

Crystal structure of human Cu-Zn Superoxide Dismutase 1 in complex with 1,2,10-Decanetriol

Aouti, S., Padmanabhan, B.

To be published.

Macromolecule Content

Total Structure Weight: 162.35 kDa
Atom Count: 12,184
Modeled Residue Count: 1,518
Deposited Residue Count: 1,540
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Cu-Zn]	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	154	Homo sapiens	Mutation(s): 0 Gene Names: SOD1 EC: 1.15.1.1 (PDB Primary Data), 1.8 (UniProt)
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00441
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1LYN (Subject of Investigation/LOI) Query on A1LYN Download:Ideal Coordinates CCD File SDF format, chain Z [auth F] SDF format, chain T [auth C] SDF format, chain Q [auth B] SDF format, chain O [auth B] SDF format, chain M [auth A] SDF format, chain GA [auth J] SDF format, chain FA [auth J] SDF format, chain DA [auth I] SDF format, chain BA [auth H] MOL2 format, chain Z [auth F] MOL2 format, chain T [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain O [auth B] MOL2 format, chain M [auth A] MOL2 format, chain GA [auth J] MOL2 format, chain FA [auth J] MOL2 format, chain DA [auth I] MOL2 format, chain BA [auth H] mmCIF format, chain Z [auth F] mmCIF format, chain T [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain O [auth B] mmCIF format, chain M [auth A] mmCIF format, chain GA [auth J] mmCIF format, chain FA [auth J] mmCIF format, chain DA [auth I] mmCIF format, chain BA [auth H]	BA [auth H] DA [auth I] FA [auth J] GA [auth J] M [auth A] BA [auth H], DA [auth I], FA [auth J], GA [auth J], M [auth A], O [auth B], Q [auth B], T [auth C], Z [auth F]	(2S)-decane-1,2,10-triol C₁₀ H₂₂ O₃ RHINSRUDDXGHLV-JTQLQIEISA-N		Interactions Focus chain BA [auth H] Focus chain DA [auth I] Focus chain FA [auth J] Focus chain GA [auth J] Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain Z [auth F] Interactions & Density Focus chain BA [auth H] Focus chain DA [auth I] Focus chain FA [auth J] Focus chain GA [auth J] Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain Z [auth F]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Y [auth F] SDF format, chain V [auth D] SDF format, chain S [auth C] SDF format, chain P [auth B] SDF format, chain L [auth A] MOL2 format, chain Y [auth F] MOL2 format, chain V [auth D] MOL2 format, chain S [auth C] MOL2 format, chain P [auth B] MOL2 format, chain L [auth A] mmCIF format, chain Y [auth F] mmCIF format, chain V [auth D] mmCIF format, chain S [auth C] mmCIF format, chain P [auth B] mmCIF format, chain L [auth A]	L [auth A], P [auth B], S [auth C], V [auth D], Y [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain Y [auth F] Interactions & Density Focus chain L [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain Y [auth F]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain X [auth F] SDF format, chain W [auth E] SDF format, chain U [auth D] SDF format, chain R [auth C] SDF format, chain N [auth B] SDF format, chain K [auth A] SDF format, chain EA [auth J] SDF format, chain CA [auth I] SDF format, chain AA [auth H] MOL2 format, chain X [auth F] MOL2 format, chain W [auth E] MOL2 format, chain U [auth D] MOL2 format, chain R [auth C] MOL2 format, chain N [auth B] MOL2 format, chain K [auth A] MOL2 format, chain EA [auth J] MOL2 format, chain CA [auth I] MOL2 format, chain AA [auth H] mmCIF format, chain X [auth F] mmCIF format, chain W [auth E] mmCIF format, chain U [auth D] mmCIF format, chain R [auth C] mmCIF format, chain N [auth B] mmCIF format, chain K [auth A] mmCIF format, chain EA [auth J] mmCIF format, chain CA [auth I] mmCIF format, chain AA [auth H]	AA [auth H] CA [auth I] EA [auth J] K [auth A] N [auth B] AA [auth H], CA [auth I], EA [auth J], K [auth A], N [auth B], R [auth C], U [auth D], W [auth E], X [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth H] Focus chain CA [auth I] Focus chain EA [auth J] Focus chain K [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain W [auth E] Focus chain X [auth F] Interactions & Density Focus chain AA [auth H] Focus chain CA [auth I] Focus chain EA [auth J] Focus chain K [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain W [auth E] Focus chain X [auth F]