6JIT

Complex structure of an imine reductase at 2.05 Angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb6JIT/pdb

Classification: OXIDOREDUCTASE
Organism(s): Stackebrandtia nassauensis DSM 44728
Expression System: Escherichia coli K-12
Mutation(s): Yes

Deposited: 2019-02-23 Released: 2020-02-26
Deposition Author(s): Li, H., Wu, L., Zheng, G.W., Zhou, J.H.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.219
R-Value Work: 0.190
R-Value Observed: 0.191

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Complex structure of an imine reductase at 2.05 Angstrom resolution

Li, H., Wu, L., Zheng, G.W., Zhou, J.H.

To be published.

Macromolecule Content

Total Structure Weight: 94.41 kDa
Atom Count: 7,060
Modelled Residue Count: 863
Deposited Residue Count: 897
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-phosphogluconate dehydrogenase NAD-binding protein	A, B, C	299	Stackebrandtia nassauensis DSM 44728	Mutation(s): 3 Gene Names: Snas_4330
UniProt
Find proteins for D3Q3R0 (Stackebrandtia nassauensis (strain DSM 44728 / CIP 108903 / NRRL B-16338 / NBRC 102104 / LLR-40K-21)) Explore D3Q3R0 Go to UniProtKB: D3Q3R0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D3Q3R0
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download Ideal Coordinates CCD File SDF format, chain F [auth C] MOL2 format, chain F [auth C]	F [auth C]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Ligand Interaction
LW7 Query on LW7 Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B]	E [auth B]	1-(2-phenylethyl)-3,4-dihydroisoquinoline C₁₇ H₁₇ N GDEYQNLNJXESFX-UHFFFAOYSA-N		Ligand Interaction
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.219
R-Value Work: 0.190
R-Value Observed: 0.191
Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.598	α = 90
b = 106.598	β = 90
c = 168.343	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-02-26

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	21878085
National Natural Science Foundation of China	China	21536004

Revision History (Full details and data files)

Version 1.0: 2020-02-26
Type: Initial release

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.