5NFJ

Crystal structure of the methyltransferase subunit of human mitochondrial Ribonuclease P (MRPP1) bound to S-adenosyl-methionine (SAM)

PDB DOI: https://doi.org/10.2210/pdb5NFJ/pdb

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

Deposited: 2017-03-14 Released: 2018-05-16
Deposition Author(s): Oerum, S., Kopec, J., Fitzpatrick, F., Newman, J.A., Chalk, R., Shrestha, L., Fairhead, M., Talon, R., Burgess-Brown, N., von Delft, F., Arrowsmith, C., Edwards, C., Bountra, C., Oppermann, U., Yue, W.W., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free: 0.206
R-Value Work: 0.185
R-Value Observed: 0.186

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of the methyltransferase subunit of human mitochondrial Ribonuclease P (MRPP1) bound to S-adenosyl-methionine (SAM)

Oerum, S., Kopec, J., Fitzpatrick, F., Newman, J.A., Oppermann, U., Yue, W.W.

To be published.

Macromolecule Content

Total Structure Weight: 73.49 kDa
Atom Count: 4,772
Modelled Residue Count: 533
Deposited Residue Count: 606
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial ribonuclease P protein 1	A, B, C	202	Homo sapiens	Mutation(s): 0 Gene Names: TRMT10C, MRPP1, RG9MTD1 EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q7L0Y3 (Homo sapiens) Explore Q7L0Y3 Go to UniProtKB: Q7L0Y3
PHAROS: Q7L0Y3 GTEx: ENSG00000174173
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7L0Y3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM Query on SAM Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] SDF format, chain P [auth C] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain P [auth C]	D [auth A], J [auth B], P [auth C]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Focus chain P [auth C] Interactions & Density Focus chain D [auth A] Focus chain J [auth B] Focus chain P [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain Q [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C]	E [auth A] F [auth A] G [auth A] K [auth B] L [auth B] E [auth A], F [auth A], G [auth A], K [auth B], L [auth B], M [auth B], Q [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B]	H [auth A], I [auth A], N [auth B], O [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B]