SMTL ID : 4trf.1

Crystal structure of Macrophage Migration Inhibitory Factor in complex with N-(pyridin-3-ylmethyl)thioformamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

homo-trimer

Ligands

3 x 35J: N-(pyridin-3-ylmethyl)thioformamide(Covalent)

35J.1: 7 residues within 4Å: Chain A: P.1, M.2, K.32, Y.36, H.62, F.113 Chain C: Y.95 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.36 Water bridges: A:I.64 35J.5: 6 residues within 4Å: Chain A: Y.95 Chain B: P.1, M.2, Y.36, F.113 Ligands: GOL.7 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.113 Hydrogen bonds: B:Y.36 Water bridges: B:I.64 35J.9: 8 residues within 4Å: Chain B: Y.95 Chain C: P.1, M.2, K.32, Y.36, H.62, I.64, F.113 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.64 Hydrogen bonds: C:Y.36 Water bridges: C:I.64 pi-Stacking: C:F.113

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: G.68, G.69, A.70, Q.71 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.69, A:A.70, A:Q.71, A:Q.71 SO4.6: 4 residues within 4Å: Chain B: G.68, G.69, A.70, Q.71 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.69, B:A.70, B:Q.71, B:Q.71 Water bridges: B:I.67 SO4.10: 4 residues within 4Å: Chain C: G.68, G.69, A.70, Q.71 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.69, C:A.70, C:Q.71, C:Q.71

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: N.109, N.110 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.109, A:N.109, A:N.110 GOL.7: 3 residues within 4Å: Chain B: K.32, Y.36 Ligands: 35J.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.32 Water bridges: B:K.32

2 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.4: 2 residues within 4Å: Chain A: A.70, R.73 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.70 Hydrogen bonds: A:R.73 IPA.8: 2 residues within 4Å: Chain B: A.70, R.73 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pantouris, G. et al., An Analysis of MIF Structural Features that Control Functional Activation of CD74. Chem.Biol. (2015)

Release Date

2015-09-30

Peptides

Macrophage migration inhibitory factor: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Macrophage migration inhibitory factor

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