7XX3

Crystal structure of human Superoxide Dismutase (SOD1) in complex with a fungal metabolite molecule, Phialomustin B (PB)

PDB DOI: https://doi.org/10.2210/pdb7XX3/pdb

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

Deposited: 2022-05-28 Released: 2023-12-13
Deposition Author(s): Padmanabhan, B., Unni, S.
Funding Organization(s): Indian Council of Medical Research, Department of Science & Technology (DST, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.230
R-Value Work: 0.199
R-Value Observed: 0.200

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Phialomustin-B a fungal metabolite isolated from Phialophora mustea modulates Superoxide Dismutase 1 (SOD1) aggregation: Therapeutic potential in Amyotrophic lateral sclerosis (ALS)

Unni, S., Padmanabhan, B.

To be published.

Macromolecule Content

Total Structure Weight: 192.83 kDa
Atom Count: 12,385
Modelled Residue Count: 1,506
Deposited Residue Count: 1,800
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Cu-Zn]	A B C [auth D] D [auth C] E [auth H] A, B, C [auth D], D [auth C], E [auth H], 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
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
I2G (Subject of Investigation/LOI) Query on I2G Download Ideal Coordinates CCD File SDF format, chain CA [auth I] SDF format, chain N [auth B] SDF format, chain S [auth D] SDF format, chain V [auth C] MOL2 format, chain CA [auth I] MOL2 format, chain N [auth B] MOL2 format, chain S [auth D] MOL2 format, chain V [auth C] mmCIF format, chain CA [auth I] mmCIF format, chain N [auth B] mmCIF format, chain S [auth D] mmCIF format, chain V [auth C]	CA [auth I], N [auth B], S [auth D], V [auth C]	(2~{E},4~{E},6~{S})-4,6-dimethyldeca-2,4-dienoic acid C₁₂ H₂₀ O₂ DZXNZBWYVLLUAX-IVONAZQTSA-N		Interactions Focus chain CA [auth I] Focus chain N [auth B] Focus chain S [auth D] Focus chain V [auth C] Interactions & Density Focus chain CA [auth I] Focus chain N [auth B] Focus chain S [auth D] Focus chain V [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain T [auth D] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain T [auth D] mmCIF format, chain L [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain T [auth D]	L [auth A], O [auth B], P [auth B], Q [auth B], T [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth D] Interactions & Density Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth D]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain X [auth E] MOL2 format, chain X [auth E] mmCIF format, chain X [auth E]	X [auth E]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain X [auth E] Interactions & Density Focus chain X [auth E]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain BA [auth I] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain R [auth D] SDF format, chain U [auth C] SDF format, chain W [auth H] SDF format, chain Y [auth E] SDF format, chain Z [auth F] MOL2 format, chain AA [auth G] MOL2 format, chain BA [auth I] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain R [auth D] MOL2 format, chain U [auth C] MOL2 format, chain W [auth H] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth F] mmCIF format, chain AA [auth G] mmCIF format, chain BA [auth I] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain R [auth D] mmCIF format, chain U [auth C] mmCIF format, chain W [auth H] mmCIF format, chain Y [auth E] mmCIF format, chain Z [auth F]	AA [auth G] BA [auth I] K [auth A] M [auth B] R [auth D] AA [auth G], BA [auth I], K [auth A], M [auth B], R [auth D], U [auth C], W [auth H], Y [auth E], Z [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain BA [auth I] Focus chain K [auth A] Focus chain M [auth B] Focus chain R [auth D] Focus chain U [auth C] Focus chain W [auth H] Focus chain Y [auth E] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth I] Focus chain K [auth A] Focus chain M [auth B] Focus chain R [auth D] Focus chain U [auth C] Focus chain W [auth H] Focus chain Y [auth E] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.230
R-Value Work: 0.199
R-Value Observed: 0.200
Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 242.445	α = 90
b = 242.445	β = 90
c = 144.491	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-12-13

Deposition Author(s):

Padmanabhan, B.

Unni, S.

Funding Organization	Location	Grant Number
Indian Council of Medical Research	India	Indian Council of Medical Research (ICMR),
Department of Science & Technology (DST, India)	India	DST-FIST: SR/FST/LS-I/2017(C)