5X1O

PI(4,5)P2 lipid binding induced a reorientation of FGF2 molecules near membrane surface to facilitate the unconventional oligomerization-dependent secretion process as revealed by a combined FTIR/NMR/X-ray study

PDB DOI: https://doi.org/10.2210/pdb5X1O/pdb

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

Deposited: 2017-01-26 Released: 2018-03-07
Deposition Author(s): Tsao, Y.H.
Funding Organization(s): Ministry of Science and Technology, R.O.C

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.276
R-Value Work: 0.225
R-Value Observed: 0.227

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

PI(4,5)P2 lipid binding induced a reorientation of FGF2 molecules near membrane surface to facilitate the unconventional oligomerization-dependent secretion process as revealed by a combined FTIR/NMR/X-ray study

Tsao, Y.H.

To be published.

Macromolecule Content

Total Structure Weight: 33.71 kDa
Atom Count: 2,291
Modelled Residue Count: 254
Deposited Residue Count: 292
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibroblast growth factor 2	A, B	146	Homo sapiens	Mutation(s): 0 Gene Names: FGF2, FGFB
UniProt & NIH Common Fund Data Resources
Find proteins for P09038 (Homo sapiens) Explore P09038 Go to UniProtKB: P09038
PHAROS: P09038 GTEx: ENSG00000138685
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09038
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
I3P Query on I3P Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE C₆ H₁₅ O₁₅ P₃ MMWCIQZXVOZEGG-XJTPDSDZSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.276
R-Value Work: 0.225
R-Value Observed: 0.227
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.616	α = 90
b = 67.346	β = 90
c = 122.196	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-03-07

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology, R.O.C	Taiwan	MOST-103-2311-B-007-011-MY3

Revision History (Full details and data files)

Version 1.0: 2018-03-07
Type: Initial release
Version 1.1: 2024-10-30
Changes: Data collection, Database references, Structure summary

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.