5YTU | pdb_00005ytu

Structure of human SOD1 complexed with isoproteranol in C2221 space group

PDB DOI: https://doi.org/10.2210/pdb5YTU/pdb

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

Deposited: 2017-11-20 Released: 2018-11-21
Deposition Author(s): Manjula, R., Padmanabhan, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.221 (Depositor), 0.222 (DCC)
R-Value Work:
0.179 (Depositor), 0.179 (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 1.2 of the entry. See complete history.

Literature

Assessment of ligand binding at a site relevant to SOD1 oxidation and aggregation

Manjula, R., Wright, G.S.A., Strange, R.W., Padmanabhan, B.

(2018) FEBS Lett 592: 1725-1737

PubMed: 29679384 Search on PubMed
DOI: https://doi.org/10.1002/1873-3468.13055
Primary Citation Related Structures:
5YTO, 5YTU, 5YUL

PubMed Abstract:
Cu/Zn superoxide dismutase-1 (SOD1) mutations are causative for a subset of amyotrophic lateral sclerosis (ALS) cases. These mutations lead to structural instability, aggregation and ultimately motor neuron death. We have determined crystal structures of SOD1 in complex with a naphthalene-catechol-linked compound which binds with low micro-molar affinity to a site important for oxidative damage-induced aggregation. SOD1 Trp32 oxidation is indeed significantly inhibited by ligand binding. Our work shows how compound linking can be applied successfully to ligand interactions on the SOD1 surface to generate relatively good binding strength. The ligand, positioned in a region important for SOD1 fibrillation, offers the possibility that it, or a similar compound, could prevent the abnormal self-association that drives SOD1 toxicity in ALS.

Organizational Affiliation

Department of Biophysics, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India.

Macromolecule Content

Total Structure Weight: 192.46 kDa
Atom Count: 12,743
Modeled Residue Count: 1,508
Deposited Residue Count: 1,800
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 [auth H] C [auth B] D [auth C] E [auth D] A, B [auth H], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F], H [auth G], I, J	180	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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5FW Query on 5FW Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	ISOPRENALINE C₁₁ H₁₇ N O₃ JWZZKOKVBUJMES-NSHDSACASA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
TAM Query on TAM Download:Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	TRIS(HYDROXYETHYL)AMINOMETHANE C₇ H₁₇ N O₃ GKODZWOPPOTFGA-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
S4P Query on S4P Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain T [auth C] SDF format, chain W [auth E] MOL2 format, chain N [auth A] MOL2 format, chain T [auth C] MOL2 format, chain W [auth E] mmCIF format, chain N [auth A] mmCIF format, chain T [auth C] mmCIF format, chain W [auth E]	N [auth A], T [auth C], W [auth E]	Dihydrogen tetrasulfide H₂ S₄ IKRMQEUTISXXQP-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain T [auth C] Focus chain W [auth E] Interactions & Density Focus chain N [auth A] Focus chain T [auth C] Focus chain W [auth E]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain P [auth H] SDF format, chain R [auth B] MOL2 format, chain P [auth H] MOL2 format, chain R [auth B] mmCIF format, chain P [auth H] mmCIF format, chain R [auth B]	P [auth H], R [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain P [auth H] Focus chain R [auth B] Interactions & Density Focus chain P [auth H] Focus chain R [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain O [auth H] SDF format, chain Q [auth B] SDF format, chain S [auth C] SDF format, chain U [auth D] SDF format, chain V [auth E] SDF format, chain X [auth F] SDF format, chain Y [auth I] SDF format, chain Z [auth J] MOL2 format, chain L [auth A] MOL2 format, chain O [auth H] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth E] MOL2 format, chain X [auth F] MOL2 format, chain Y [auth I] MOL2 format, chain Z [auth J] mmCIF format, chain L [auth A] mmCIF format, chain O [auth H] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth C] mmCIF format, chain U [auth D] mmCIF format, chain V [auth E] mmCIF format, chain X [auth F] mmCIF format, chain Y [auth I] mmCIF format, chain Z [auth J]	L [auth A] O [auth H] Q [auth B] S [auth C] U [auth D] L [auth A], O [auth H], Q [auth B], S [auth C], U [auth D], V [auth E], X [auth F], Y [auth I], Z [auth J]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain O [auth H] Focus chain Q [auth B] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth E] Focus chain X [auth F] Focus chain Y [auth I] Focus chain Z [auth J] Interactions & Density Focus chain L [auth A] Focus chain O [auth H] Focus chain Q [auth B] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth E] Focus chain X [auth F] Focus chain Y [auth I] Focus chain Z [auth J]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.221 (Depositor), 0.222 (DCC)
R-Value Work: 0.179 (Depositor), 0.179 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 164.521	α = 90
b = 203.791	β = 90
c = 144.771	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2018-11-21

Deposition Author(s):

Manjula, R.

Padmanabhan, B.

Revision History (Full details and data files)

Version 1.0: 2018-11-21
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary