6FWB

Crystal structure of Mat2A at 1.79 Angstron resolution

PDB DOI: https://doi.org/10.2210/pdb6FWB/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2018-03-06 Released: 2019-03-27
Deposition Author(s): Zhou, A., Wei, Z., Bai, J., Wang, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.183
R-Value Work: 0.172
R-Value Observed: 0.172

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Identification of a natural inhibitor of methionine adenosyltransferase 2A regulating one-carbon metabolism in keratinocytes.

Bai, J., Gao, Y., Chen, L., Yin, Q., Lou, F., Wang, Z., Xu, Z., Zhou, H., Li, Q., Cai, W., Sun, Y., Niu, L., Wang, H., Wei, Z., Lu, S., Zhou, A., Zhang, J., Wang, H.

(2019) EBioMedicine 39: 575-590

PubMed: 30591370 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1016/j.ebiom.2018.12.036
Primary Citation of Related Structures:
6FWB

PubMed Abstract:
Psoriasis is a common chronic inflammatory skin disease which lacks effective strategies for the treatment. Natural compounds with biological activities are good tools to identify new targets with therapeutic potentials. Acetyl-11-keto-β-boswellic acid (AKBA) is the most bioactive ingredient of boswellic acids, a group of compounds with anti-inflammatory and anti-cancer properties. Target identification of AKBA and metabolomics analysis of psoriasis helped to elucidate the molecular mechanism underlying its effect, and provide new target(s) to treat the disease.

Organizational Affiliation

Department of Immunology and Microbiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai Institute of Immunology, Shanghai 200025, China.

Macromolecule Content

Total Structure Weight: 185.5 kDa
Atom Count: 12,195
Modelled Residue Count: 1,472
Deposited Residue Count: 1,640
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-adenosylmethionine synthase isoform type-2	A [auth B], B [auth A], C, D	410	Homo sapiens	Mutation(s): 0 Gene Names: MAT2A, AMS2, MATA2 EC: 2.5.1.6
UniProt & NIH Common Fund Data Resources
Find proteins for P31153 (Homo sapiens) Explore P31153 Go to UniProtKB: P31153
PHAROS: P31153 GTEx: ENSG00000168906
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P31153
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain GA [auth D] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth C] SDF format, chain FA [auth D] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain GA [auth D] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B]	FA [auth D] GA [auth D] L [auth B] M [auth B] X [auth A] FA [auth D], GA [auth D], L [auth B], M [auth B], X [auth A], Y [auth A], Z [auth C]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain FA [auth D] Focus chain GA [auth D] Focus chain L [auth B] Focus chain M [auth B] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth C] Interactions & Density Focus chain FA [auth D] Focus chain GA [auth D] Focus chain L [auth B] Focus chain M [auth B] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain DA [auth D] SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain P [auth A] SDF format, chain S [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain CA [auth D] SDF format, chain EA [auth D] SDF format, chain G [auth B] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain T [auth A] MOL2 format, chain BA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain P [auth A] MOL2 format, chain S [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain CA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain G [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain T [auth A]	BA [auth D] CA [auth D] DA [auth D] E [auth B] EA [auth D] BA [auth D], CA [auth D], DA [auth D], E [auth B], EA [auth D], F [auth B], G [auth B], H [auth B], I [auth B], J [auth B], K [auth B], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain E [auth B] Focus chain EA [auth D] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain E [auth B] Focus chain EA [auth D] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain O [auth A] MOL2 format, chain AA [auth D] MOL2 format, chain O [auth A]	AA [auth D], O [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain O [auth A] Interactions & Density Focus chain AA [auth D] Focus chain O [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B]	N [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]