4IIO

Crystal Structure of the Second SH3 Domain of ITSN2 Bound with a Synthetic Peptide

PDB DOI: https://doi.org/10.2210/pdb4IIO/pdb

Classification: ENDOCYTOSIS
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2012-12-20 Released: 2013-12-25
Deposition Author(s): Dong, A., Guan, X., Huang, H., Gu, J., Tempel, W., Sidhu, S., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Tong, Y., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.226
R-Value Work: 0.194
R-Value Observed: 0.195

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of the Second SH3 Domain of ITSN2 Bound with a Synthetic Peptide

Guan, X., Dong, A., Huang, H., Gu, J., Tempel, W., Sidhu, S., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Tong, Y.

To be published.

Macromolecule Content

Total Structure Weight: 16.26 kDa
Atom Count: 1,323
Modelled Residue Count: 133
Deposited Residue Count: 145
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Intersectin-2	A, B	66	Homo sapiens	Mutation(s): 0 Gene Names: ITSN2, KIAA1256, SH3D1B, SWAP
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZM3 (Homo sapiens) Explore Q9NZM3 Go to UniProtKB: Q9NZM3
PHAROS: Q9NZM3 GTEx: ENSG00000198399
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NZM3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Synthetic Peptide	C	13	N/A	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth C], T [auth C]	UNKNOWN ATOM OR ION X		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] 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] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] 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] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.226
R-Value Work: 0.194
R-Value Observed: 0.195
Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.053	α = 90
b = 48.053	β = 90
c = 112.435	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
JDirector	data collection
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing
Coot	model building

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-12-25

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2013-12-25
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2021-03-10
Changes: Advisory, Database references, Derived calculations
Version 1.3: 2023-09-20
Changes: Data collection, Database references, Refinement description