5P9X | pdb_00005p9x

humanized rat catechol O-methyltransferase in complex with N-[1-[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]propan-2-yl]-5-(4-fluorophenyl)-2,3-dihydroxybenzamide

PDB DOI: https://doi.org/10.2210/pdb5P9X/pdb
Deposition Group: G_1002014 | Explore G_1002014

Classification: TRANSFERASE
Organism(s): Rattus norvegicus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2016-10-19 Released: 2017-11-22
Deposition Author(s): Ehler, A., Lerner, C., Rudolph, M.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.12 Å
R-Value Free:
0.184 (Depositor), 0.194 (DCC)
R-Value Work:
0.160 (Depositor), 0.169 (DCC)
R-Value Observed:
0.161 (Depositor)

Starting Model: other
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of a COMT complex

Lerner, C., Jakob-Roetne, R., Groebke-Zbinden, K., Buettelmann, B., Rudolph, M.G.

To be published.

Macromolecule Content

Total Structure Weight: 25.62 kDa
Atom Count: 2,098
Modeled Residue Count: 213
Deposited Residue Count: 221
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catechol O-methyltransferase	A	221	Rattus norvegicus	Mutation(s): 2 Gene Names: Comt EC: 2.1.1.6
UniProt
Find proteins for P22734 (Rattus norvegicus) Explore P22734 Go to UniProtKB: P22734
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22734
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7JO Query on 7JO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	N-[1-[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]propan-2-yl]-5-(4-fluorophenyl)-2,3-dihydroxybenzamide C₂₅ H₂₅ F N₆ O₆ PQAIDYIFCYLFAS-RGJCZRFTSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
NHE Query on NHE Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C₈ H₁₇ N O₃ S MKWKNSIESPFAQN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.12 Å
R-Value Free: 0.184 (Depositor), 0.194 (DCC)
R-Value Work: 0.160 (Depositor), 0.169 (DCC)
R-Value Observed: 0.161 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.964	α = 90
b = 54.087	β = 90
c = 80.776	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2017-11-22

Deposition Author(s):

Ehler, A.

Lerner, C.

Rudolph, M.G.

Revision History (Full details and data files)

Version 1.0: 2017-11-22
Type: Initial release
Version 1.1: 2018-02-21
Changes: Structure summary
Version 1.2: 2021-11-17
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 2024-04-03
Changes: Data collection, Refinement description