6KDR | pdb_00006kdr

Crystal structure of human NRMT2 in complex with human centromere protein B peptide

PDB DOI: https://doi.org/10.2210/pdb6KDR/pdb

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

Deposited: 2019-07-02 Released: 2020-07-08
Deposition Author(s): Yue, Y., Li, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free:
0.205 (Depositor), 0.200 (DCC)
R-Value Work:
0.178 (Depositor), 0.190 (DCC)
R-Value Observed:
0.189 (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

Substrate-enzyme engagement regulates state-specific alpha-N methylation of NRMT2

Wu, R., Yue, Y., Zheng, X., Li, H.

To be published.

Macromolecule Content

Total Structure Weight: 58.4 kDa
Atom Count: 3,935
Modelled Residue Count: 455
Deposited Residue Count: 506
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha N-terminal protein methyltransferase 1B	A, B	244	Homo sapiens	Mutation(s): 0 Gene Names: METTL11B, C1orf184, NRMT2 EC: 2.1.1.299
UniProt & NIH Common Fund Data Resources
Find proteins for Q5VVY1 (Homo sapiens) Explore Q5VVY1 Go to UniProtKB: Q5VVY1
GTEx: ENSG00000203740
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5VVY1
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide from Major centromere autoantigen B	C [auth D], D [auth E]	9	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P07199 (Homo sapiens) Explore P07199 Go to UniProtKB: P07199
PHAROS: P07199 GTEx: ENSG00000125817
Entity Groups
UniProt Group	P07199
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH (Subject of Investigation/LOI) Query on SAH Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	F [auth A], I [auth B], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B]
CL (Subject of Investigation/LOI) Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain L [auth E] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth E] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth E]	G [auth A], K [auth B], L [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth E] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth E]