4PKK | pdb_00004pkk

Crystal structure of Macrophage Migration inhibitory factor in complex with furan-2-ylmethyl)imino methanethiol

PDB DOI: https://doi.org/10.2210/pdb4PKK/pdb

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

Deposited: 2014-05-14 Released: 2016-05-04
Deposition Author(s): Pantouris, G., Lolis, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free:
0.181 (Depositor), 0.192 (DCC)
R-Value Work:
0.162 (Depositor), 0.174 (DCC)
R-Value Observed:
0.163 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Crystal structure of Macrophage Migration inhibitory factor with a covalent inhibitor

Pantouris, G., Lolis, E.

To be published.

Macromolecule Content

Total Structure Weight: 38.39 kDa
Atom Count: 2,985
Modeled Residue Count: 341
Deposited Residue Count: 342
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14174
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
31E Query on 31E Download:Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain J [auth B] SDF format, chain D [auth A] MOL2 format, chain P [auth C] MOL2 format, chain J [auth B] MOL2 format, chain D [auth A] mmCIF format, chain P [auth C] mmCIF format, chain J [auth B] mmCIF format, chain D [auth A]	D [auth A], J [auth B], P [auth C]	(Z)-[(furan-2-ylmethyl)imino]methanethiol C₆ H₇ N O S BDAKRWHGDWIWEU-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Focus chain P [auth C] Interactions & Density Focus chain D [auth A] Focus chain J [auth B] Focus chain P [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A], L [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A], K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B]
IPA Query on IPA Download:Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B]	M [auth B], N [auth B], O [auth B], Q [auth C]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Interactions & Density Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.181 (Depositor), 0.192 (DCC)
R-Value Work: 0.162 (Depositor), 0.174 (DCC)
R-Value Observed: 0.163 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.702	α = 90
b = 95.702	β = 90
c = 103.662	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-05-04

Deposition Author(s):

Pantouris, G.

Lolis, E.

Revision History (Full details and data files)

Version 1.0: 2016-05-04
Type: Initial release
Version 1.1: 2017-11-22
Changes: Derived calculations, Refinement description
Version 1.2: 2023-12-27
Changes: Data collection, Database references, Refinement description
Version 2.0: 2024-12-25
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary

4PKK | pdb_00004pkk

Crystal structure of Macrophage Migration inhibitory factor in complex with furan-2-ylmethyl)imino methanethiol

Literature

Crystal structure of Macrophage Migration inhibitory factor with a covalent inhibitor

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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