24GZ | pdb_000024gz

Artificial Copper-binding trimeric protein 1 (Cu(I)TP6)

PDB DOI: https://doi.org/10.2210/pdb24GZ/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Methanococcus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2026-03-03 Released: 2026-07-15
Deposition Author(s): Choi, I.S., Song, W.J.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free:
0.267 (Depositor), 0.265 (DCC)
R-Value Work:
0.209 (Depositor), 0.207 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
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Literature

Artificial Copper-binding trimeric protein 1 (Cu(I)TP6)

Choi, I.S., Song, W.J.

To be published.

Macromolecule Content

Total Structure Weight: 85.82 kDa
Atom Count: 5,853
Modeled Residue Count: 700
Deposited Residue Count: 753
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphosulfolactate synthase	A, B, C	251	Methanococcus	Mutation(s): 0 Gene Names: comA, MJ0255 EC: 4.4.1.19
UniProt
Find proteins for Q57703 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q57703 Go to UniProtKB: Q57703
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q57703
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS (Subject of Investigation/LOI) Query on TRS Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
CU1 (Subject of Investigation/LOI) Query on CU1 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C]	D [auth A], F [auth B], G [auth C]	COPPER (I) ION Cu VMQMZMRVKUZKQL-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth C] Interactions & Density Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
BP5 Query on BP5	A, B, C	L-PEPTIDE LINKING	C₁₃ H₁₃ N₃ O₂		ALA

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free: 0.267 (Depositor), 0.265 (DCC)
R-Value Work: 0.209 (Depositor), 0.207 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.256	α = 90
b = 115.256	β = 90
c = 38.969	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-07-15

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History (Full details and data files)

Version 1.0: 2026-07-15
Type: Initial release

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