5U6G | pdb_00005u6g

Crystal Structure of the holo Domain-Swapped Dimer mutant Q108K:K40D Human Cellular Retinol Binding Protein II bound with all trans retinal

PDB DOI: https://doi.org/10.2210/pdb5U6G/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens
Expression System: Bacteria
Mutation(s): Yes

Deposited: 2016-12-08 Released: 2017-10-18
Deposition Author(s): Assar, Z., Geiger, J.H.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.281 (Depositor), 0.278 (DCC)
R-Value Work:
0.177 (Depositor), 0.179 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of the holo Domain-Swapped Dimer mutant Q108K:K40D Human Cellular Retinol Binding Protein II bound with all trans retinal

Assar, Z., Geiger, J.H.

To be published.

Macromolecule Content

Total Structure Weight: 190.17 kDa
Atom Count: 13,551
Modeled Residue Count: 1,596
Deposited Residue Count: 1,596
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinol-binding protein 2	A B C D E [auth H] A, B, C, D, E [auth H], F [auth E], G [auth F], J, K, L	133	Homo sapiens	Mutation(s): 2 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P50120
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinol-binding protein 2	H [auth G], I	133	Homo sapiens	Mutation(s): 1 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P50120
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RET Query on RET Download:Ideal Coordinates CCD File SDF format, chain W [auth L] SDF format, chain V [auth K] SDF format, chain U [auth I] SDF format, chain T [auth G] SDF format, chain S [auth F] SDF format, chain R [auth E] SDF format, chain Q [auth H] SDF format, chain P [auth D] SDF format, chain O [auth C] SDF format, chain N [auth B] SDF format, chain M [auth A] MOL2 format, chain W [auth L] MOL2 format, chain V [auth K] MOL2 format, chain U [auth I] MOL2 format, chain T [auth G] MOL2 format, chain S [auth F] MOL2 format, chain R [auth E] MOL2 format, chain Q [auth H] MOL2 format, chain P [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth A] mmCIF format, chain W [auth L] mmCIF format, chain V [auth K] mmCIF format, chain U [auth I] mmCIF format, chain T [auth G] mmCIF format, chain S [auth F] mmCIF format, chain R [auth E] mmCIF format, chain Q [auth H] mmCIF format, chain P [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth A]	M [auth A] N [auth B] O [auth C] P [auth D] Q [auth H] M [auth A], N [auth B], O [auth C], P [auth D], Q [auth H], R [auth E], S [auth F], T [auth G], U [auth I], V [auth K], W [auth L]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth H] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth G] Focus chain U [auth I] Focus chain V [auth K] Focus chain W [auth L] Interactions & Density Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth H] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth G] Focus chain U [auth I] Focus chain V [auth K] Focus chain W [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.281 (Depositor), 0.278 (DCC)
R-Value Work: 0.177 (Depositor), 0.179 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.474	α = 90
b = 73.597	β = 90
c = 351.601	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-10-18

Deposition Author(s):

Assar, Z.

Geiger, J.H.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2017-10-18
Type: Initial release
Version 1.1: 2022-03-23
Changes: Advisory, Author supporting evidence, Database references, Derived calculations
Version 1.2: 2023-10-04
Changes: Data collection, Refinement description
Version 1.3: 2024-11-20
Changes: Structure summary