4QT6 | pdb_00004qt6

Crystal structure of the SPRY domain of human HERC1

PDB DOI: https://doi.org/10.2210/pdb4QT6/pdb

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

Deposited: 2014-07-07 Released: 2015-01-07
Deposition Author(s): Dong, A., Hu, J., Guan, X., Wernimont, A., Li, Y., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Tong, Y., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free:
0.212 (Depositor), 0.224 (DCC)
R-Value Work:
0.170 (Depositor), 0.181 (DCC)
R-Value Observed:
0.171 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of the SPRY domain of human HERC1

Hu, J., Dong, A., Guan, X., Wernimont, A., Li, Y., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Tong, Y.

To be published.

Macromolecule Content

Total Structure Weight: 18.31 kDa
Atom Count: 1,491
Modeled Residue Count: 159
Deposited Residue Count: 159
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable E3 ubiquitin-protein ligase HERC1	A	159	Homo sapiens	Mutation(s): 0 Gene Names: HERC1 EC: 2.3.2.26
UniProt & NIH Common Fund Data Resources
Find proteins for Q15751 (Homo sapiens) Explore Q15751 Go to UniProtKB: Q15751
PHAROS: Q15751 GTEx: ENSG00000103657
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15751
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ARF Query on ARF Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	FORMAMIDE C H₃ N O ZHNUHDYFZUAESO-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	UNKNOWN ATOM OR ION X		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free: 0.212 (Depositor), 0.224 (DCC)
R-Value Work: 0.170 (Depositor), 0.181 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.73	α = 90
b = 99.73	β = 90
c = 99.73	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SOLVE	phasing
RESOLVE	phasing
Coot	model building
ARP/wARP	model building

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-01-07

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2015-01-07
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary