3A7E

Crystal structure of human COMT complexed with SAM and 3,5-dinitrocatechol

PDB DOI: https://doi.org/10.2210/pdb3A7E/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-09-26 Released: 2010-09-15
Deposition Author(s): Tsuji, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.298
R-Value Work: 0.218
R-Value Observed: 0.226

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Hit to Lead: Comprehensive Strategy of de novo Scaffold Generation by FBDD. Part 1: In silico Fragments Linking and Verification of Spatial Proximity using Inter Ligand NOE Approachs

Nonaka, Y., Momose, T., Ozawa, T., Ozawa, M., Nakatsu, M., Tsuji, E., Okazaki, K., Takase, Y., Kiyotani, T.

To be published.

Macromolecule Content

Total Structure Weight: 24.65 kDa
Atom Count: 1,748
Modelled Residue Count: 212
Deposited Residue Count: 216
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	216	Homo sapiens	Mutation(s): 0 Gene Names: COMT EC: 2.1.1.6
UniProt & NIH Common Fund Data Resources
Find proteins for P21964 (Homo sapiens) Explore P21964 Go to UniProtKB: P21964
PHAROS: P21964 GTEx: ENSG00000093010
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P21964
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM Query on SAM Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
DNC Query on DNC Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	3,5-DINITROCATECHOL C₆ H₄ N₂ O₆ VDCDWNDTNSWDFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density 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]	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: 2.80 Å
R-Value Free: 0.298
R-Value Work: 0.218
R-Value Observed: 0.226
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.909	α = 90
b = 50.909	β = 90
c = 168.186	γ = 120

Software Package:

Software Name	Purpose
BSS	data collection
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-09-15

Deposition Author(s):

Tsuji, E.

Revision History (Full details and data files)

Version 1.0: 2010-09-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

Prepare Data

Validate Data

Deposit Data

Help and Resources

3A7E

Crystal structure of human COMT complexed with SAM and 3,5-dinitrocatechol

Hit to Lead: Comprehensive Strategy of de novo Scaffold Generation by FBDD. Part 1: In silico Fragments Linking and Verification of Spatial Proximity using Inter Ligand NOE Approachs

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)