4LEC | pdb_00004lec

Human Methyltransferase-Like Protein 21A

PDB DOI: https://doi.org/10.2210/pdb4LEC/pdb

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

Deposited: 2013-06-25 Released: 2013-07-17
Deposition Author(s): Dong, A., Zeng, H., Fenner, M., Wernimont, A., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Brown, P.J., Wu, H., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free:
0.256 (Depositor), 0.237 (DCC)
R-Value Work:
0.219 (Depositor), 0.213 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

The Crystal Structure of Human Methyltransferase-Like Protein 21A in Complex with SAH

Zeng, H., Dong, A., Wu, H.

To be published.

Macromolecule Content

Total Structure Weight: 48.54 kDa
Atom Count: 3,368
Modeled Residue Count: 403
Deposited Residue Count: 424
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein-lysine methyltransferase METTL21A	A, B	212	Homo sapiens	Mutation(s): 0 Gene Names: METTL21A, FAM119A, HCA557B EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WXB1 (Homo sapiens) Explore Q8WXB1 Go to UniProtKB: Q8WXB1
PHAROS: Q8WXB1 GTEx: ENSG00000144401
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8WXB1
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free: 0.256 (Depositor), 0.237 (DCC)
R-Value Work: 0.219 (Depositor), 0.213 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.166	α = 90
b = 72.166	β = 90
c = 102.954	γ = 120

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
JDirector	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing
BUSTER	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-07-17

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2013-07-17
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description