5UNA

Fragment of 7SK snRNA methylphosphate capping enzyme

PDB DOI: https://doi.org/10.2210/pdb5UNA/pdb
Entry: 5UNA supersedes: 3G07

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

Deposited: 2017-01-30 Released: 2017-03-08
Deposition Author(s): Wu, H., Tempel, W., Dombrovski, L., McCarthy, A.A., Loppnau, P., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Park, H., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.217
R-Value Work: 0.204
R-Value Observed: 0.204

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Fragment of 7SK snRNA methylphosphate capping enzyme

Wu, H., Tempel, W., Dombrovski, L., McCarthy, A.A., Loppnau, P., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Park, H., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 204.91 kDa
Atom Count: 9,632
Modelled Residue Count: 1,277
Deposited Residue Count: 1,782
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
7SK snRNA methylphosphate capping enzyme	A, B, C, D, E A, B, C, D, E, F	292	Homo sapiens	Mutation(s): 0 Gene Names: MEPCE, BCDIN3 EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q7L2J0 (Homo sapiens) Explore Q7L2J0 Go to UniProtKB: Q7L2J0
PHAROS: Q7L2J0 GTEx: ENSG00000146834
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7L2J0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
unidentified peptide section/fragment	G [auth M], H [auth N], I [auth O], J [auth Q], K [auth R]	6	Homo sapiens	Mutation(s): 0
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 L [auth A] SDF format, chain M [auth B] SDF format, chain N [auth C] SDF format, chain O [auth D] SDF format, chain P [auth E] SDF format, chain Q [auth F] MOL2 format, chain L [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth F] mmCIF format, chain L [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth D] mmCIF format, chain P [auth E] mmCIF format, chain Q [auth F]	L [auth A] M [auth B] N [auth C] O [auth D] P [auth E] L [auth A], M [auth B], N [auth C], O [auth D], P [auth E], Q [auth F]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain L [auth A] Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth E] Focus chain Q [auth F]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.217
R-Value Work: 0.204
R-Value Observed: 0.204
Space Group: H 3
Diffraction Data: https://doi.org/10.18430/M35UNA

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 183.24	α = 90
b = 183.24	β = 90
c = 151.39	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SOLVE	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-03-08

Deposition Author(s):

Structural Genomics Consortium (SGC)

This entry supersedes: 3G07

Revision History (Full details and data files)

Version 1.0: 2017-03-08
Type: Initial release
Version 1.1: 2024-10-23
Changes: Data collection, Database references, Experimental preparation, Structure summary