1RBP

CRYSTALLOGRAPHIC REFINEMENT OF HUMAN SERUM RETINOL BINDING PROTEIN AT 2 ANGSTROMS RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb1RBP/pdb

Classification: RETINOL TRANSPORT
Organism(s): Homo sapiens
Mutation(s): No
Membrane Protein: Yes OPM

Deposited: 1990-04-02 Released: 1991-07-15
Deposition Author(s): Jones, T.A., Newcomer, M.E., Cowan, S.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Work: 0.181

wwPDB Validation 3D Report Full Report

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

Literature

Crystallographic refinement of human serum retinol binding protein at 2A resolution.

Cowan, S.W., Newcomer, M.E., Jones, T.A.

(1990) Proteins 8: 44-61

PubMed: 2217163 Search on PubMed
DOI: https://doi.org/10.1002/prot.340080108
Primary Citation of Related Structures:
1RBP

PubMed Abstract:
Human serum retinol binding protein (RBP) in complex with retinol has been crystallographically refined to an R-factor of 18.1% with 2A resolution data. The protein topology results in an anti-parallel beta-barrel that encapsulates the retinol ligand. A detailed description of the protein and the binding site is provided. Our structural work has helped to define a family of proteins, many of which are carrier proteins for smaller ligand molecules. We describe the structural basis for the conservation of sequence within the family.

Organizational Affiliation

Department of Molecular Biology, Biomedicum Centre, Uppsala, Sweden.

Macromolecule Content

Total Structure Weight: 21.27 kDa
Atom Count: 1,582
Modelled Residue Count: 175
Deposited Residue Count: 182
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PLASMA RETINOL-BINDING PROTEIN PRECURSOR	A	182	Homo sapiens	Mutation(s): 0 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P02753 (Homo sapiens) Explore P02753 Go to UniProtKB: P02753
PHAROS: P02753 GTEx: ENSG00000138207
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02753
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RTL Query on RTL Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	RETINOL C₂₀ H₃₀ O FPIPGXGPPPQFEQ-OVSJKPMPSA-N		Interactions Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
RTL	Binding MOAD: 1RBP	Kd: 190 (nM) from 1 assay(s)
RTL	PDBBind: 1RBP	Kd: 190 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Work: 0.181
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.7	α = 90
b = 48.7	β = 90
c = 76.5	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 1991-07-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1991-07-15
Type: Initial release
Version 1.1: 2008-03-03
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-11-29
Changes: Derived calculations, Other

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.