7Y8O | pdb_00007y8o

Structure of ScIRED-R3-V4 from Streptomyces clavuligerus in complex with 5-(3-fluorophenyl)-3,4-dihydro-2H-pyrrole

PDB DOI: https://doi.org/10.2210/pdb7Y8O/pdb

Classification: HYDROLASE/INHIBITOR
Organism(s): Streptomyces clavuligerus
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2022-06-24 Released: 2023-03-22
Deposition Author(s): Zhang, L.L., Liu, W.D., Shi, M., Huang, J.W., Yang, Y., Chen, C.C., Guo, R.T.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.227 (Depositor), 0.228 (DCC)
R-Value Work:
0.186 (Depositor), 0.188 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Structure of ScIRED-R3-V4 from Streptomyces clavuligerus in complex with 5-(3-fluorophenyl)-3,4-dihydro-2H-pyrrole

Zhang, L.L., Liu, W.D., Shi, M., Huang, J.W., Yang, Y., Chen, C.C., Guo, R.T.

To be published.

Macromolecule Content

Total Structure Weight: 62.5 kDa
Atom Count: 4,681
Modeled Residue Count: 573
Deposited Residue Count: 580
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SciR	A, B	290	Streptomyces clavuligerus	Mutation(s): 0
UniProt
Find proteins for E2PUR9 (Streptomyces clavuligerus) Explore E2PUR9 Go to UniProtKB: E2PUR9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E2PUR9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP (Subject of Investigation/LOI) Query on NAP Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
Q0R (Subject of Investigation/LOI) Query on Q0R Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	2-[2,5-bis(fluoranyl)phenyl]pyrrolidine C₁₀ H₁₁ F₂ N NCXSNNVYILYEBC-SNVBAGLBSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.227 (Depositor), 0.228 (DCC)
R-Value Work: 0.186 (Depositor), 0.188 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.797	α = 90
b = 81.358	β = 90
c = 93.127	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
SAINT	data reduction
SADABS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-03-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-03-22
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection
Version 1.2: 2023-11-29
Changes: Refinement description
Version 1.3: 2024-04-03
Changes: Database references

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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.