5X1O | pdb_00005x1o

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 (Depositor), 0.276 (DCC)
R-Value Work:
0.225 (Depositor), 0.225 (DCC)
R-Value Observed:
0.227 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5X1O

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
Modeled Residue Count: 254
Deposited Residue Count: 292
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [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 (Depositor), 0.276 (DCC)
R-Value Work: 0.225 (Depositor), 0.225 (DCC)
R-Value Observed: 0.227 (Depositor)

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

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Ligand Structure Quality Assessment

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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

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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.