9DDU | pdb_00009ddu

Q108K:K40L:T51V:T53C:R58Y:Y19W:Q38L:Q4A:T29L mutant of hCRBPII bound to FR1V and irradiated with UV light at pH 3.0

PDB DOI: https://doi.org/10.2210/pdb9DDU/pdb

Classification: RETINOL BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-08-28 Released: 2025-02-12
Deposition Author(s): Bingham, C., Geiger, J.H.
Funding Organization(s): National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.218 (Depositor), 0.221 (DCC)
R-Value Work:
0.193 (Depositor), 0.195 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Photoswitching fluorescence via a novel Trp-flap mechanism

Bingham, C., Ehyeai, N., Maity, S., Cantrell, J., Gwasdacus, J., Sheng, W., Vasileiou, C., Borhan, B., Geiger, J.H.

To be published.

Macromolecule Content

Total Structure Weight: 32.63 kDa
Atom Count: 2,409
Modelled Residue Count: 266
Deposited Residue Count: 266
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinol-binding protein 2	A [auth B], B [auth A]	133	Homo sapiens	Mutation(s): 8 Gene Names: RBP2, CRBP2
UniProt & NIH Common Fund Data Resources
Find proteins for P50120 (Homo sapiens) Explore P50120 Go to UniProtKB: P50120
PHAROS: P50120 GTEx: ENSG00000114113
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P50120
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZFJ (Subject of Investigation/LOI) Query on ZFJ Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain J [auth A] MOL2 format, chain C [auth B] MOL2 format, chain J [auth A] mmCIF format, chain C [auth B] mmCIF format, chain J [auth A]	C [auth B], J [auth A]	(4aP)-N,N-diethyl-9,9-dimethyl-7-[(1E)-prop-1-en-1-yl]-9H-fluoren-2-amine C₂₂ H₂₇ N UMARKYXLRJLTSK-RMKNXTFCSA-N		Interactions Focus chain C [auth B] Focus chain J [auth A] Interactions & Density Focus chain C [auth B] Focus chain J [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain O [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain O [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain O [auth A]	E [auth B] F [auth B] G [auth B] H [auth B] I [auth B] E [auth B], F [auth B], G [auth B], H [auth B], I [auth B], K [auth A], L [auth A], O [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth A] Interactions & Density Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth A]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain M [auth A] SDF format, chain N [auth A] MOL2 format, chain D [auth B] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] mmCIF format, chain D [auth B] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A]	D [auth B], M [auth A], N [auth A]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain D [auth B] Focus chain M [auth A] Focus chain N [auth A]