6OPL

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)
R-Value Work:
0.232 (Depositor)
R-Value Observed:
0.233 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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
Modelled Residue Count: 205
Deposited Residue Count: 205
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P30043
Sequence Annotations Expand
Reference Sequence LOADING

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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.37 Å
R-Value Free: 0.262 (Depositor)
R-Value Work: 0.232 (Depositor)
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

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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 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.