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), 0.280 (DCC)
R-Value Work:
0.177 (Depositor), 0.180 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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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

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P50120
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 M [auth A] SDF format, chain N [auth B] SDF format, chain O [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth H] SDF format, chain S [auth F] SDF format, chain T [auth G] SDF format, chain V [auth K] SDF format, chain W [auth L] SDF format, chain U [auth I] SDF format, chain R [auth E] MOL2 format, chain M [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth H] MOL2 format, chain S [auth F] MOL2 format, chain T [auth G] MOL2 format, chain V [auth K] MOL2 format, chain W [auth L] MOL2 format, chain U [auth I] MOL2 format, chain R [auth E] mmCIF format, chain M [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth H] mmCIF format, chain S [auth F] mmCIF format, chain T [auth G] mmCIF format, chain V [auth K] mmCIF format, chain W [auth L] mmCIF format, chain U [auth I] mmCIF format, chain R [auth E]	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), 0.280 (DCC)
R-Value Work: 0.177 (Depositor), 0.180 (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

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Ligand Structure Quality Assessment

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