3SYX

Crystal Structure of the WH1 domain from human sprouty-related, EVH1 domain-containing protein. Northeast Structural Genomics Consortium Target HR5538B.

PDB DOI: https://doi.org/10.2210/pdb3SYX/pdb

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

Deposited: 2011-07-18 Released: 2011-08-03
Deposition Author(s): Vorobiev, S., Su, M., Seetharaman, J., Sahdev, S., Xiao, R., Ciccosanti, C., Shastry, R., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.271
R-Value Work: 0.228
R-Value Observed: 0.230

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of the WH1 domain from human sprouty-related, EVH1 domain-containing protein.

Vorobiev, S., Su, M., Seetharaman, J., Sahdev, S., Xiao, R., Ciccosanti, C., Shastry, R., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 14.92 kDa
Atom Count: 955
Modelled Residue Count: 118
Deposited Residue Count: 130
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sprouty-related, EVH1 domain-containing protein 1	A	130	Homo sapiens	Mutation(s): 0 Gene Names: SPRED1
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z699 (Homo sapiens) Explore Q7Z699 Go to UniProtKB: Q7Z699
PHAROS: Q7Z699 GTEx: ENSG00000166068
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7Z699
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YT3 Query on YT3 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	YTTRIUM (III) ION Y GRTBAGCGDOYUBE-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.271
R-Value Work: 0.228
R-Value Observed: 0.230
Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.754	α = 90
b = 52.754	β = 90
c = 121.638	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-08-03

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2011-08-03
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description

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Deposit Data

Help and Resources

3SYX

Crystal Structure of the WH1 domain from human sprouty-related, EVH1 domain-containing protein. Northeast Structural Genomics Consortium Target HR5538B.

Crystal Structure of the WH1 domain from human sprouty-related, EVH1 domain-containing protein.

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)