2P02 | pdb_00002p02

Crystal structure of the alpha subunit of human S-adenosylmethionine synthetase 2

PDB DOI: https://doi.org/10.2210/pdb2P02/pdb
Entry: 2P02 supersedes: 2HJ2

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-02-28 Released: 2007-03-13
Deposition Author(s): Papagrigoriou, E., Shafqat, N., Rojkova, A., Niessen, F.H., Kavanagh, K.L., von Delft, F., Gorrec, F., Ugochukwu, E., Arrowsmith, C.H., Edwards, A., Weigelt, J., Sundstrom, M., Oppermann, U., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.21 Å
R-Value Free:
0.119 (Depositor), 0.119 (DCC)
R-Value Work:
0.100 (Depositor), 0.100 (DCC)
R-Value Observed:
0.101 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of the alpha subunit of human S-adenosylmethionine synthetase 2

Papagrigoriou, E., Shafqat, N., Rojkova, A., Niessen, F.H., Kavanagh, K.L., von Delft, F., Gorrec, F., Ugochukwu, E., Arrowsmith, C.H., Edwards, A., Weigelt, J., Sundstrom, M., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 44.24 kDa
Atom Count: 3,582
Modeled Residue Count: 380
Deposited Residue Count: 396
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-adenosylmethionine synthetase isoform type-2	A	396	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P31153
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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] mmCIF 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]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.21 Å
R-Value Free: 0.119 (Depositor), 0.119 (DCC)
R-Value Work: 0.100 (Depositor), 0.100 (DCC)
R-Value Observed: 0.101 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.301	α = 90
b = 94.106	β = 90
c = 117.383	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-03-13

Deposition Author(s):

Structural Genomics Consortium (SGC)

This entry supersedes: 2HJ2

Revision History (Full details and data files)

Version 1.0: 2007-03-13
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: 2017-10-18
Changes: Refinement description
Version 1.4: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description