SMTL ID : 5eiz.1

Crystal structure of Y99A mutant of human macrophage migration inhibitory factor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

homo-trimer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: P.1, M.2, H.62, S.63, V.106 Chain C: Y.95, N.97 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:Y.95, C:N.97, C:N.97, A:P.1, A:M.2, A:I.64 GOL.4: 8 residues within 4Å: Chain A: Y.95, N.97 Chain B: P.1, M.2, Y.36, H.62, S.63, V.106 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:N.97, A:N.97, B:P.1, B:M.2, B:H.62, B:I.64 GOL.7: 8 residues within 4Å: Chain B: Y.95, N.97 Chain C: P.1, M.2, H.62, S.63, I.64, M.101 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:I.64, B:N.97, B:N.97

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 SO4.5: 4 residues within 4Å: Chain B: G.68, G.69, A.70, Q.71 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.69, B:A.70, B:Q.71, B:Q.71 SO4.8: 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 IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.3: 2 residues within 4Å: Chain A: G.65, K.66 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.66 Hydrogen bonds: A:K.66 Water bridges: A:I.67 IPA.6: 2 residues within 4Å: Chain B: G.65, K.66 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:K.66 Hydrogen bonds: B:K.66 Water bridges: B:I.67, B:Q.71

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pantouris, G. et al., Nanosecond Dynamics Regulate the MIF-Induced Activity of CD74. Angew. Chem. Int. Ed. Engl. (2018)

Release Date

2015-11-11

Peptides

Macrophage migration inhibitory factor: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Macrophage migration inhibitory factor