SMTL ID : 7e4c.1

Crystal structure of MIF bound to compound11

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

homo-trimer

Ligands

13 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 5 residues within 4Å: Chain A: P.1, K.32, S.63, I.64 Ligands: SO4.8 Ligand excluded by PLIP CL.2: 4 residues within 4Å: Chain A: G.68, G.69, A.70, Q.71 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: M.101, N.102, N.105 Ligand excluded by PLIP CL.4: 5 residues within 4Å: Chain A: D.16, G.17, F.18, L.19, S.20 Ligand excluded by PLIP CL.5: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: M.2, H.62 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: G.68, G.69, A.70, Q.71 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain B: P.1, K.32, S.63, I.64 Ligands: SO4.15 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: M.101, N.102, N.105 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: P.33, P.34, Q.35 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain C: P.1, K.32, S.63, I.64 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain C: M.101, N.102, N.105 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain C: G.68, G.69, A.70, Q.71 Ligand excluded by PLIP

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

SO4.7: 1 residues within 4Å: Chain A: R.73 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Water bridges: B:S.111, A:R.73, A:R.73, A:R.73 Salt bridges: A:R.73 SO4.8: 5 residues within 4Å: Chain A: K.32, Y.36, F.113 Chain C: Y.95 Ligands: CL.1 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Salt bridges: A:K.32 Hydrogen bonds: C:Y.95, C:Y.95 SO4.9: 1 residues within 4Å: Chain A: W.108 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.109 SO4.15: 8 residues within 4Å: Chain A: Y.95, N.97 Chain B: P.1, M.2, H.62, S.63, V.106 Ligands: CL.11 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:P.1, B:I.64, A:N.97

1 x GBJ: 4-[(3R)-8,8-dimethyl-3,4-dihydro-2H,8H-pyrano[2,3-f]chromen-3-yl]benzene-1,3-diol(Non-covalent)

GBJ.14: 7 residues within 4Å: Chain A: F.49, D.92, Y.95 Chain B: Q.35, Y.36, W.108, F.113 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:Y.95, B:Q.35, B:Y.36, B:W.108 Water bridges: B:Q.35 pi-Stacking: B:W.108, B:F.113

1 x NA: SODIUM ION(Non-functional Binders)

NA.16: 1 residues within 4Å: Chain A: Y.99 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, L. et al., Identification and Structure-Activity Relationships of Dietary Flavonoids as Human Macrophage Migration Inhibitory Factor (MIF) Inhibitors. J.Agric.Food Chem. (2021)

Release Date

2023-02-15

Peptides

Macrophage migration inhibitory factor: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Macrophage migration inhibitory factor

Related Entries With Identical Sequence