3H2P | pdb_00003h2p

Human SOD1 D124V Variant

PDB DOI: https://doi.org/10.2210/pdb3H2P/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Saccharomyces cerevisiae
Mutation(s): Yes

Deposited: 2009-04-14 Released: 2010-05-05
Deposition Author(s): Seetharaman, S.V., Winkler, D.D., Taylor, A.B., Cao, X., Whitson, L.J., Doucette, P.A., Valentine, J.S., Carroll, M.C., Culotta, V.C., Hart, P.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.202 (Depositor), 0.194 (DCC)
R-Value Work:
0.152 (Depositor), 0.145 (DCC)
R-Value Observed:
0.155 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3H2P

This is version 1.3 of the entry. See complete history.

Literature

Structures of Pathogenic SOD1 Mutants H80R and D124V: Disrupted Zinc-binding and Compromised Post-translational Modification by the Copper Chaperone CCS

Seetharaman, S.V., Winkler, D.D., Taylor, A.B., Cao, X., Whitson, L.J., Doucette, P.A., Valentine, J.S., Carroll, M.C., Culotta, V.C., Hart, P.J.

To be published.

Macromolecule Content

Total Structure Weight: 32.07 kDa
Atom Count: 2,135
Modeled Residue Count: 255
Deposited Residue Count: 306
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Cu-Zn]	A, B	153	Homo sapiens	Mutation(s): 1 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
MLI Query on MLI Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	C [auth A], D [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B]
ACE Query on ACE Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	ACETYL GROUP C₂ H₄ O IKHGUXGNUITLKF-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.202 (Depositor), 0.194 (DCC)
R-Value Work: 0.152 (Depositor), 0.145 (DCC)
R-Value Observed: 0.155 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.919	α = 90
b = 57.972	β = 90
c = 105.021	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-05-05

Deposition Author(s):

Seetharaman, S.V.

Valentine, J.S.

Revision History (Full details and data files)

Version 1.0: 2010-05-05
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-10-13
Changes: Database references, Derived calculations
Version 1.3: 2023-09-06
Changes: Data collection, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.