SMTL ID : 6oye.1

Crystal structure of Y99F mutant of human macrophage migration inhibitory factor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

homo-trimer

Ligands

4 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 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:N.97, C:N.97, A:P.1, A:H.62, A:I.64 GOL.4: 8 residues within 4Å: Chain A: Y.95, N.97 Chain B: P.1, M.2, H.62, S.63, I.64, V.106 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.97, A:N.97, B:H.62, B:I.64 GOL.9: 10 residues within 4Å: Chain B: Y.95, N.97 Chain C: P.1, M.2, H.62, S.63, I.64, M.101, V.106 Ligands: GOL.10 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:P.1, C:H.62, C:I.64, B:N.97, B:N.97 GOL.10: 5 residues within 4Å: Chain C: P.1, K.32, I.64, F.113 Ligands: GOL.9 2 PLIP interactions: 2 interactions with chain C Water bridges: C:K.32, C:K.32

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 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.68, B:G.69, B:A.70, B:Q.71, B:Q.71 SO4.11: 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

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

IPA.3: 1 residues within 4Å: Chain A: R.86 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.86, A:R.86 IPA.6: 3 residues within 4Å: Chain B: Q.35, Y.36, W.108 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.36, B:W.108 IPA.7: 4 residues within 4Å: Chain B: G.17, F.18, L.19, S.20 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.17, B:G.17, B:L.19, B:S.20 IPA.8: 2 residues within 4Å: Chain B: A.70, R.73 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.70 Hydrogen bonds: B:R.73 Water bridges: B:A.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pantouris, G. et al., Regulation of MIF Enzymatic Activity by an Allosteric Site at the Central Solvent Channel. Cell Chem Biol (2020)

Release Date

2020-04-29

Peptides

Macrophage migration inhibitory factor: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Macrophage migration inhibitory factor