9JIY | pdb_00009jiy

Macrophage migration inhibitory factor S61H/Y100H mutant complexed with three Zinc ions (Zn3-MIF(S61H/Y100H)-L)

PDB DOI: https://doi.org/10.2210/pdb9JIY/pdb

Classification: CYTOKINE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-09-12 Released: 2025-08-06
Deposition Author(s): Himiyama, T., Okamoto, Y.
Funding Organization(s): Japan Science and Technology, Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free:
0.174 (Depositor), 0.174 (DCC)
R-Value Work:
0.155 (Depositor), 0.158 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A cytokine-based designer enzyme with an abiological multinuclear metal center exhibits intrinsic and extrinsic catalysis

Ueno, A., Takida, F., Kita, T., Ishii, T., Himiyama, T., Mabuchi, T., Okamoto, Y.

(2025) Nat Commun

DOI: https://doi.org/10.1038/s41467-025-61909-5

Macromolecule Content

Total Structure Weight: 38.82 kDa
Atom Count: 3,128
Modeled Residue Count: 342
Deposited Residue Count: 345
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrophage migration inhibitory factor	A, B, C	115	Homo sapiens	Mutation(s): 2 Gene Names: MIF, GLIF, MMIF EC: 5.3.2.1 (PDB Primary Data), 5.3.3.12 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P14174 (Homo sapiens) Explore P14174 Go to UniProtKB: P14174
PHAROS: P14174 GTEx: ENSG00000240972
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14174
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C]	F [auth A], G [auth A], L [auth B], P [auth C], Q [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain R [auth C] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C]	H [auth A], I [auth A], M [auth B], R [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain R [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain R [auth C]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain K [auth B] SDF format, chain O [auth C] MOL2 format, chain D [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] mmCIF format, chain D [auth A] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C]	D [auth A], K [auth B], O [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Focus chain O [auth C] Interactions & Density Focus chain D [auth A] Focus chain K [auth B] Focus chain O [auth C]
IPA Query on IPA Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain S [auth C] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain S [auth C] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain S [auth C]	J [auth A], N [auth B], S [auth C]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain N [auth B] Focus chain S [auth C] Interactions & Density Focus chain J [auth A] Focus chain N [auth B] Focus chain S [auth C]
CO3 (Subject of Investigation/LOI) Query on CO3 Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CARBONATE ION C O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.174 (Depositor), 0.174 (DCC)
R-Value Work: 0.155 (Depositor), 0.158 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.153	α = 90
b = 68.211	β = 90
c = 86.906	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-08-06

Deposition Author(s):

Himiyama, T.

Okamoto, Y.

Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJAX1913
Japan Science and Technology	Japan	JPMJPR22A4
Japan Science and Technology	Japan	JPMJFR212H
Japan Society for the Promotion of Science (JSPS)	Japan	21H05118
Japan Society for the Promotion of Science (JSPS)	Japan	24K08609