2AVD | pdb_00002avd

Crystal Structure of Human Catechol-O-methyltransferase domain containing 1

PDB DOI: https://doi.org/10.2210/pdb2AVD/pdb

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

Deposited: 2005-08-29 Released: 2005-09-13
Deposition Author(s): Min, J.R., Wu, H., Zeng, H., Loppnau, P., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Plotnikov, A.N., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.213 (Depositor), 0.211 (DCC)
R-Value Work:
0.172 (Depositor), 0.169 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
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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

The Crystal Structure of Human Catechol-O-methyltransferase domain containing 1 in complex with S-adenosyl-L-methionine

Min, J.R., Wu, H., Zeng, H., Loppnau, P., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Plotnikov, A.N.

To be published.

Macromolecule Content

Total Structure Weight: 51.83 kDa
Atom Count: 3,935
Modeled Residue Count: 438
Deposited Residue Count: 458
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, B	229	Homo sapiens	Mutation(s): 0 EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q86VU5 (Homo sapiens) Explore Q86VU5 Go to UniProtKB: Q86VU5
PHAROS: Q86VU5 GTEx: ENSG00000165644
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q86VU5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM Query on SAM Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.213 (Depositor), 0.211 (DCC)
R-Value Work: 0.172 (Depositor), 0.169 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.882	α = 90
b = 65.222	β = 102.66
c = 61.799	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing
ARP/wARP	model building

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2005-09-13

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2005-09-13
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description