3HVJ | pdb_00003hvj

Rat catechol O-methyltransferase in complex with a catechol-type, N6-propyladenine-containing bisubstrate inhibitor

PDB DOI: https://doi.org/10.2210/pdb3HVJ/pdb

Classification: TRANSFERASE
Organism(s): Rattus norvegicus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-06-16 Released: 2009-10-13
Deposition Author(s): Ehler, A., Schlatter, D., Stihle, M., Benz, J., Rudolph, M.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free:
0.235 (Depositor), 0.240 (DCC)
R-Value Work:
0.183 (Depositor), 0.190 (DCC)
R-Value Observed:
0.186 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Molecular recognition at the active site of catechol-o-methyltransferase: energetically favorable replacement of a water molecule imported by a bisubstrate inhibitor.

Ellermann, M., Jakob-Roetne, R., Lerner, C., Borroni, E., Schlatter, D., Roth, D., Ehler, A., Rudolph, M.G., Diederich, F.

(2009) Angew Chem Int Ed Engl 48: 9092-9096

PubMed: 19882607 Search on PubMed
DOI: https://doi.org/10.1002/anie.200904410
Primary Citation of Related Structures:
3HVH, 3HVI, 3HVJ, 3HVK

Organizational Affiliation

Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland.

Macromolecule Content

Total Structure Weight: 50.97 kDa
Atom Count: 3,910
Modelled Residue Count: 427
Deposited Residue Count: 442
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catechol O-methyltransferase	A, B	221	Rattus norvegicus	Mutation(s): 0 EC: 2.1.1.6
UniProt
Find proteins for P22734 (Rattus norvegicus) Explore P22734 Go to UniProtKB: P22734
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22734
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
705 Query on 705 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	N-[(E)-3-[(2R,3S,4R,5R)-3,4-dihydroxy-5-(6-propylaminopurin-9-yl)oxolan-2-yl]prop-2-enyl]-5-(4-fluorophenyl)-2,3-dihydroxy-benzamide C₂₈ H₂₉ F N₆ O₆ ZTSZMLSDNBUFMA-WIRSHZJASA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
BTB Query on BTB 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-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CL Query on CL 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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.235 (Depositor), 0.240 (DCC)
R-Value Work: 0.183 (Depositor), 0.190 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.346	α = 90
b = 61.414	β = 90
c = 132.5	γ = 90

Software Package:

Software Name	Purpose
COMO	phasing
REFMAC	refinement
XDS	data reduction
SADABS	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-10-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-10-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2012-08-08
Changes: Database references, Structure summary
Version 1.3: 2017-11-01
Changes: Refinement description
Version 1.4: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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Rat catechol O-methyltransferase in complex with a catechol-type, N6-propyladenine-containing bisubstrate inhibitor

Molecular recognition at the active site of catechol-o-methyltransferase: energetically favorable replacement of a water molecule imported by a bisubstrate inhibitor.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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