6FVH

Macrophage Migration Inhibitory Factor (MIF) with Covalently Bound PITC

PDB DOI: https://doi.org/10.2210/pdb6FVH/pdb

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

Deposited: 2018-03-02 Released: 2018-06-06
Deposition Author(s): Samygina, V.R., Bourenkov, G., Sokolov, A.V.
Funding Organization(s): RFBR

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.166
R-Value Work: 0.138
R-Value Observed: 0.139

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structural Study of the Complex Formed by Ceruloplasmin and Macrophage Migration Inhibitory Factor.

Sokolov, A.V., Dadinova, L.A., Petoukhov, M.V., Bourenkov, G., Dubova, K.M., Amarantov, S.V., Volkov, V.V., Kostevich, V.A., Gorbunov, N.P., Grudinina, N.A., Vasilyev, V.B., Samygina, V.R.

(2018) Biochemistry (Mosc) 83: 701-707

PubMed: 30195326 Search on PubMed
DOI: https://doi.org/10.1134/S000629791806007X
Primary Citation of Related Structures:
6FVE, 6FVH

PubMed Abstract:
Macrophage migration inhibitory factor (MIF) is a key proinflammatory cytokine. Inhibitors of tautomerase activity of MIF are perspective antiinflammatory compounds. Ceruloplasmin, the copper-containing ferroxidase of blood plasma, is a noncompetitive inhibitor of tautomerase activity of MIF in the reaction with p-hydroxyphenylpyruvate. Small-angle X-ray scattering established a model of the complex formed by MIF and ceruloplasmin. Crystallographic analysis of MIF with a modified active site supports the model. The stoichiometry of 3 CP/MIF trimer complex was established using gel filtration. Conformity of novel data concerning the interaction regions in the studied proteins with previous biochemical data is discussed.

Organizational Affiliation

Institute of Experimental Medicine, St. Petersburg, 197376, Russia.

Macromolecule Content

Total Structure Weight: 38.05 kDa
Atom Count: 3,197
Modelled Residue Count: 342
Deposited Residue Count: 342
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	114	Homo sapiens	Mutation(s): 0 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0FI Query on 0FI Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C]	E [auth A], I [auth B], K [auth C]	N-phenylthioformamide C₇ H₇ N S UNRRVOATHRPYDX-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain K [auth C] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain K [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain J [auth B] SDF format, chain L [auth C] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C]	D [auth A] F [auth A] G [auth B] H [auth B] J [auth B] D [auth A], F [auth A], G [auth B], H [auth B], J [auth B], L [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth B] Focus chain L [auth C] Interactions & Density Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth B] Focus chain L [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.166
R-Value Work: 0.138
R-Value Observed: 0.139
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.822	α = 90
b = 68.375	β = 90
c = 88.596	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-06-06

Deposition Author(s):

Samygina, V.R.

Bourenkov, G.

Sokolov, A.V.

Funding Organization	Location	Grant Number
RFBR	Russian Federation	15-54-74006

Revision History (Full details and data files)

Version 1.0: 2018-06-06
Type: Initial release
Version 1.1: 2018-09-19
Changes: Data collection, Database references
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-11-13
Changes: Structure summary