5WCF | pdb_00005wcf

Human HMT1 hnRNP methyltransferase-like protein 6 (S. cerevisiae)

PDB DOI: https://doi.org/10.2210/pdb5WCF/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: unidentified baculovirus
Mutation(s): No

Deposited: 2017-06-30 Released: 2017-08-02
Deposition Author(s): Dong, A., Zeng, H., Hutch, A., Seitova, A., Walker, J.R., 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: 1.98 Å
R-Value Free:
0.208 (Depositor), 0.218 (DCC)
R-Value Work:
0.200 (Depositor), 0.205 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
View more details

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 HMT1 hnRNP methyltransferase-like protein 6 in complex with MTLLE1441

Zeng, H., Dong, A., Hutch, A., Seitova, A., Walker, J.R., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Brown, P.J., Wu, H., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 43.02 kDa
Atom Count: 2,768
Modeled Residue Count: 319
Deposited Residue Count: 376
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein arginine N-methyltransferase 6	A	376	Homo sapiens	Mutation(s): 0 Gene Names: PRMT6, HRMT1L6 EC: 2.1.1.319
UniProt & NIH Common Fund Data Resources
Find proteins for Q96LA8 (Homo sapiens) Explore Q96LA8 Go to UniProtKB: Q96LA8
PHAROS: Q96LA8 GTEx: ENSG00000198890
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96LA8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A0S Query on A0S 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]	(5R)-4-(5-bromofuran-2-carbonyl)-5-(4-fluorophenyl)-7-methyl-1,3,4,5-tetrahydro-2H-1,4-benzodiazepin-2-one C₂₁ H₁₆ Br F N₂ O₃ IPHKQIFYQWJQAB-HXUWFJFHSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SAH Query on SAH 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]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
144 Query on 144 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	TRIS-HYDROXYMETHYL-METHYL-AMMONIUM C₄ H₁₂ N O₃ DRDCQJADRSJFFD-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
A0S	BindingDB: 5WCF	IC50: 388 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.208 (Depositor), 0.218 (DCC)
R-Value Work: 0.200 (Depositor), 0.205 (DCC)
R-Value Observed: 0.200 (Depositor)

Diffraction Data:

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.721	α = 90
b = 94.721	β = 90
c = 108.713	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-08-02

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2017-08-02
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-12-25
Changes: Data collection, Derived calculations, Structure summary