9QR0 | pdb_00009qr0

Cobalamin-binding chimera 1 (Cob01)

PDB DOI: https://doi.org/10.2210/pdb9QR0/pdb

Classification: DE NOVO PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-04-02 Released: 2026-10-14
Deposition Author(s): Romero-Romero, S., Koch, J.-S., Toledo-Patino, S., Hoecker, B.
Funding Organization(s): European Research Council (ERC), Volkswagen Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free:
0.227 (Depositor), 0.228 (DCC)
R-Value Work:
0.180 (Depositor), 0.183 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9QR0

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

Literature

Cobalamin-binding chimeras designed by fold recombination

Koch, J.-S., Romero-Romero, S., Toledo-Patino, S., Braun, A.E., Hoecker, B.

To be published.

Macromolecule Content

Total Structure Weight: 31.71 kDa
Atom Count: 2,351
Modeled Residue Count: 273
Deposited Residue Count: 286
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coenzyme B12-dependent mutase,Uroporphyrinogen-III synthase	A	286	Homo sapiens	Mutation(s): 1 Gene Names: APE_1686.1, Mgu, UROS EC: 4.2.1.75
UniProt & NIH Common Fund Data Resources
Find proteins for Q9YBB1 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Explore Q9YBB1 Go to UniProtKB: Q9YBB1
Find proteins for P10746 (Homo sapiens) Explore P10746 Go to UniProtKB: P10746
PHAROS: P10746 GTEx: ENSG00000188690
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	Q9YBB1 P10746
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG 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]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free: 0.227 (Depositor), 0.228 (DCC)
R-Value Work: 0.180 (Depositor), 0.183 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.61	α = 90
b = 43.2	β = 108.22
c = 65.69	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-14

Deposition Author(s):

Romero-Romero, S.

Toledo-Patino, S.

Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	647548 Protein Lego
Volkswagen Foundation	Germany	94747

Revision History (Full details and data files)

Version 1.0: 2026-10-14
Type: Initial release