2IIP | pdb_00002iip

Human Nicotinamide N-methyltransferase

PDB DOI: https://doi.org/10.2210/pdb2IIP/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2006-09-28 Released: 2006-10-10
Deposition Author(s): Bernstein, G., Min, J., Wu, H., Tempel, W., Zeng, H., Loppnau, P., Avvakumov, G.V., Wasney, G., Weigelt, J., 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: 2.05 Å
R-Value Free:
0.265 (Depositor), 0.257 (DCC)
R-Value Work:
0.217 (Depositor), 0.216 (DCC)
R-Value Observed:
0.219 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

The Crystal Structure of Human Nicotinamide N-methyltransferase in complex with SAH

Bernstein, G., Min, J., Wu, H., Tempel, W., Zeng, H., Loppnau, P., Avvakumov, G.V., Wasney, G., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Plotnikov, A.N.

To be published.

Macromolecule Content

Total Structure Weight: 127.4 kDa
Atom Count: 8,481
Modeled Residue Count: 1,031
Deposited Residue Count: 1,132
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicotinamide N-methyltransferase	A, B, C, D	283	Homo sapiens	Mutation(s): 3 Gene Names: NNMT EC: 2.1.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P40261 (Homo sapiens) Explore P40261 Go to UniProtKB: P40261
PHAROS: P40261 GTEx: ENSG00000166741
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40261
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.265 (Depositor), 0.257 (DCC)
R-Value Work: 0.217 (Depositor), 0.216 (DCC)
R-Value Observed: 0.219 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.016	α = 82.35
b = 62.007	β = 81.89
c = 107.073	γ = 68.3

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-10-10

Deposition Author(s):

Avvakumov, G.V.

Arrowsmith, C.H.

Plotnikov, A.N.

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2006-10-10
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: 2018-03-07
Changes: Data collection
Version 1.4: 2021-10-20
Changes: Database references, Derived calculations
Version 1.5: 2024-02-21
Changes: Data collection

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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.