SMTL ID : 8imr.1

Structure of ligand-free human macrophage migration inhibitory factor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-trimer

Ligands

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

SO4.1: 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 SO4.4: 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

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 6 residues within 4Å: Chain A: P.1, Y.36, S.63, I.64, F.113 Chain B: Y.95 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.63, A:I.64 EDO.3: 3 residues within 4Å: Chain A: G.51, S.52, S.53 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.53, A:S.53 Water bridges: A:S.52 EDO.5: 3 residues within 4Å: Chain B: S.20, E.21, Q.24 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.21 EDO.6: 5 residues within 4Å: Chain A: Y.95 Chain C: P.1, Y.36, I.64 Ligands: EDO.8 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:P.1, C:I.64 EDO.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.8: 6 residues within 4Å: Chain A: Y.95, N.97 Chain C: M.2, H.62, V.106 Ligands: EDO.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.97

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

IPA.9: 1 residues within 4Å: Chain C: G.65 No protein-ligand interaction detected (PLIP) IPA.10: 3 residues within 4Å: Chain C: Q.35, Y.36, W.108 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Q.35, C:Y.36, C:W.108 IPA.11: 4 residues within 4Å: Chain C: G.68, G.69, A.70, Q.71 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:A.70 Hydrogen bonds: C:A.70, C:Q.71, C:Q.71

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sugishima, K. et al., Identification of methotrexate as an inhibitor of macrophage migration inhibitory factor by high-resolution crystal structure analysis. To Be Published

Release Date

2024-03-13

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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