9MRS | pdb_00009mrs

Crystal structure of human MMACHC in complex with MMADHC and B12

PDB DOI: https://doi.org/10.2210/pdb9MRS/pdb

Classification: METAL TRANSPORT
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-01-08 Released: 2026-03-18
Deposition Author(s): Mascarenhas, R., Banerjee, R.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free:
0.357 (Depositor), 0.343 (DCC)
R-Value Work:
0.300 (Depositor), 0.306 (DCC)
R-Value Observed:
0.300 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 9MRS

Ligand Structure Quality Assessment

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

Literature

Structural and Biophysical Characterization of Thiolato-Cobalamin

Ruetz, M., Mascarenhas, R., Banerjee, R.

To be published.

Macromolecule Content

Total Structure Weight: 239.95 kDa
Atom Count: 11,661
Modeled Residue Count: 1,420
Deposited Residue Count: 2,076
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyanocobalamin reductase / alkylcobalamin dealkylase	A, C [auth B], D [auth E], F [auth G]	223	Homo sapiens	Mutation(s): 0 Gene Names: MMACHC EC: 2.5.1.151 (PDB Primary Data), 1.16.1.6 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y4U1 (Homo sapiens) Explore Q9Y4U1 Go to UniProtKB: Q9Y4U1
PHAROS: Q9Y4U1 GTEx: ENSG00000132763
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y4U1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cobalamin trafficking protein CblD	B [auth D], E [auth F], G [auth C], H	296	Homo sapiens	Mutation(s): 0 Gene Names: MMADHC, C2orf25, CL25022, HSPC161, My011
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H3L0 (Homo sapiens) Explore Q9H3L0 Go to UniProtKB: Q9H3L0
PHAROS: Q9H3L0 GTEx: ENSG00000168288
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9H3L0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 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 L [auth G] SDF format, chain K [auth E] SDF format, chain J [auth B] SDF format, chain I [auth A] MOL2 format, chain L [auth G] MOL2 format, chain K [auth E] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] mmCIF format, chain L [auth G] mmCIF format, chain K [auth E] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A]	I [auth A], J [auth B], K [auth E], L [auth G]	COBALAMIN C₆₂ H₈₉ Co N₁₃ O₁₄ P LKVIQTCSMMVGFU-DWSMJLPVSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth E] Focus chain L [auth G] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth E] Focus chain L [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.357 (Depositor), 0.343 (DCC)
R-Value Work: 0.300 (Depositor), 0.306 (DCC)
R-Value Observed: 0.300 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.764	α = 90
b = 67.983	β = 99.38
c = 192.66	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-03-18

Deposition Author(s):

Mascarenhas, R.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	DK045776

Revision History (Full details and data files)

Version 1.0: 2026-03-18
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.