6OPL | pdb_00006opl

Human biliverdin IX beta reductase Q14R mutant: NADP complex

PDB DOI: https://doi.org/10.2210/pdb6OPL/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2019-04-25 Released: 2020-04-29
Deposition Author(s): Paukovich, N.A., Eisenmesser, E.Z.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.37 Å
R-Value Free:
0.262 (Depositor), 0.258 (DCC)
R-Value Work:
0.232 (Depositor), 0.229 (DCC)
R-Value Observed:
0.233 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6OPL

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Controlling biliverdin reductase B coenzyme binding through evolution

Paukovich, N.A., Eisenmesser, E.Z.

To be published.

Macromolecule Content

Total Structure Weight: 22.79 kDa
Atom Count: 1,844
Modeled Residue Count: 205
Deposited Residue Count: 205
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flavin reductase (NADPH)	A	205	Homo sapiens	Mutation(s): 1 Gene Names: BLVRB, FLR EC: 1.5.1.30 (PDB Primary Data), 1.3.1.24 (PDB Primary Data), 2.6.99 (UniProt), 1.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P30043 (Homo sapiens) Explore P30043 Go to UniProtKB: P30043
PHAROS: P30043 GTEx: ENSG00000090013
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P30043
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.37 Å
R-Value Free: 0.262 (Depositor), 0.258 (DCC)
R-Value Work: 0.232 (Depositor), 0.229 (DCC)
R-Value Observed: 0.233 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.163	α = 90
b = 98.145	β = 90
c = 125.853	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-04-29

Deposition Author(s):

Paukovich, N.A.

Eisenmesser, E.Z.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	--

Revision History (Full details and data files)

Version 1.0: 2020-04-29
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.