9CBR | pdb_00009cbr

Methionine synthase from Thermus thermophilus HB8, Homocysteine, Folate, and Cobalamin Domains, Catalytic Conformation (Hcy-on)

PDB DOI: https://doi.org/10.2210/pdb9CBR/pdb

Classification: TRANSFERASE
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-06-19 Released: 2025-06-25
Deposition Author(s): Yamada, K., Menjdoza, J., Koutmos, M.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free:
0.248 (Depositor), 0.246 (DCC)
R-Value Work:
0.236 (Depositor), 0.236 (DCC)
R-Value Observed:
0.237 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Methionine synthase from Thermus thermophilus HB8, Homocysteine, Folate, and Cobalamin Domains, Catalytic Conformation (Hcy-on)

Menjdoza, J., Yamada, K., Koutmos, M.

To be published.

Macromolecule Content

Total Structure Weight: 97.29 kDa
Atom Count: 7,010
Modeled Residue Count: 867
Deposited Residue Count: 874
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine synthase	A	874	Thermus thermophilus HB8	Mutation(s): 11 Gene Names: TTHA0618 EC: 2.1.1.13
UniProt
Find proteins for Q5SKM5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKM5 Go to UniProtKB: Q5SKM5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5SKM5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B12 (Subject of Investigation/LOI) Query on B12 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]	COBALAMIN C₆₂ H₈₉ Co N₁₃ O₁₄ P LKVIQTCSMMVGFU-DWSMJLPVSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
C2F (Subject of Investigation/LOI) Query on C2F 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]	5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID C₂₀ H₂₅ N₇ O₆ ZNOVTXRBGFNYRX-STQMWFEESA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A]	C [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain E [auth A]
K (Subject of Investigation/LOI) Query on K Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]