4KGN | pdb_00004kgn

Crystal structure of a tRNA (cytidine(34)-2'-O)-methyltransferase bound to S-adenosyl homocysteine

PDB DOI: https://doi.org/10.2210/pdb4KGN/pdb

Classification: TRANSFERASE
Organism(s): Burkholderia pseudomallei 1710b
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-04-29 Released: 2013-05-08
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.193 (Depositor), 0.190 (DCC)
R-Value Work:
0.169 (Depositor), 0.180 (DCC)
R-Value Observed:
0.170 (Depositor)

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 a TrmH family tRNA methyltransferase bound to S-adenosyl homocysteine

Edwards, T.E., Fairman, J.W., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecule Content

Total Structure Weight: 143.94 kDa
Atom Count: 9,713
Modeled Residue Count: 1,220
Deposited Residue Count: 1,280
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (cytidine(34)-2'-O)-methyltransferase	A, B, C, D, E A, B, C, D, E, F, G, H	160	Burkholderia pseudomallei 1710b	Mutation(s): 0 Gene Names: BURPS1710b_0668, trmL EC: 2.1.1.207
UniProt
Find proteins for Q3JWH1 (Burkholderia pseudomallei (strain 1710b)) Explore Q3JWH1 Go to UniProtKB: Q3JWH1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3JWH1
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 Q [auth G] SDF format, chain N [auth E] SDF format, chain L [auth C] SDF format, chain I [auth A] MOL2 format, chain Q [auth G] MOL2 format, chain N [auth E] MOL2 format, chain L [auth C] MOL2 format, chain I [auth A] mmCIF format, chain Q [auth G] mmCIF format, chain N [auth E] mmCIF format, chain L [auth C] mmCIF format, chain I [auth A]	I [auth A], L [auth C], N [auth E], Q [auth G]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain I [auth A] Focus chain L [auth C] Focus chain N [auth E] Focus chain Q [auth G] Interactions & Density Focus chain I [auth A] Focus chain L [auth C] Focus chain N [auth E] Focus chain Q [auth G]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain R [auth G] SDF format, chain P [auth F] SDF format, chain O [auth E] SDF format, chain M [auth C] SDF format, chain K [auth B] SDF format, chain J [auth A] MOL2 format, chain R [auth G] MOL2 format, chain P [auth F] MOL2 format, chain O [auth E] MOL2 format, chain M [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth A] mmCIF format, chain R [auth G] mmCIF format, chain P [auth F] mmCIF format, chain O [auth E] mmCIF format, chain M [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth A]	J [auth A] K [auth B] M [auth C] O [auth E] P [auth F] J [auth A], K [auth B], M [auth C], O [auth E], P [auth F], R [auth G]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth E] Focus chain P [auth F] Focus chain R [auth G] Interactions & Density Focus chain J [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth E] Focus chain P [auth F] Focus chain R [auth G]