SMTL ID : 5b4o.1

Crystal structure of Macrophage Migration Inhibitory Factor in complex with BTZO-14

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.37 Å

Oligo State

homo-trimer

Ligands

4 x 6DQ: 2-pyridin-3-yl-1,3-benzothiazin-4-one(Non-covalent)

6DQ.1: 12 residues within 4Å: Chain A: P.1, M.2, K.32, Y.36, H.62, S.63, I.64, M.101, V.106, F.113 Chain B: Y.95, N.97 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:K.32, A:H.62, A:I.64, A:V.106, A:F.113 Hydrogen bonds: A:P.1, A:K.32, A:I.64 pi-Stacking: A:Y.36, B:Y.95 6DQ.8: 12 residues within 4Å: Chain B: P.1, M.2, K.32, Y.36, H.62, S.63, I.64, M.101, V.106, F.113 Chain C: Y.95, N.97 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:K.32, B:Y.36, B:Y.36, B:H.62, B:I.64, B:V.106 Hydrogen bonds: B:I.64 pi-Stacking: B:F.113, C:Y.95 6DQ.9: 6 residues within 4Å: Chain B: Q.35, Y.36, W.108, F.113 Chain C: F.49, Y.95 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:Y.36, B:W.108, B:F.113, C:Y.95 Hydrogen bonds: B:Q.35 Water bridges: B:Y.36 pi-Stacking: B:W.108 6DQ.13: 12 residues within 4Å: Chain A: Y.95, N.97 Chain C: P.1, M.2, K.32, Y.36, H.62, S.63, I.64, M.101, V.106, F.113 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:K.32, C:Y.36, C:Y.36, C:H.62, C:I.64, C:M.101, C:V.106, C:V.106, C:F.113 Hydrogen bonds: C:K.32, C:I.64 pi-Stacking: A:Y.95

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

EDO.2: 2 residues within 4Å: Chain A: K.66, Q.71 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.66, A:I.67, A:Q.71 Water bridges: A:I.67, A:I.67, A:Q.71

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

SO4.3: 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: 2 residues within 4Å: Chain A: A.70, R.73 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.73 Salt bridges: A:R.73 SO4.5: 1 residues within 4Å: Chain A: K.77 No protein-ligand interaction detected (PLIP) SO4.6: 5 residues within 4Å: Chain A: Q.45 Chain B: V.42, Q.45 Chain C: V.42, Q.45 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: B:Q.45, C:Q.45, A:Q.45 Water bridges: B:Q.45 SO4.7: 6 residues within 4Å: Chain A: H.62, Y.99 Chain B: H.62, Y.99 Chain C: H.62, Y.99 11 PLIP interactions: 3 interactions with chain A, 5 interactions with chain C, 3 interactions with chain B Water bridges: A:H.62, A:Y.99, C:S.60, C:S.60, C:H.62, C:H.62, B:Y.99 Salt bridges: A:H.62, C:H.62, B:H.62 Hydrogen bonds: B:Y.99 SO4.10: 1 residues within 4Å: Chain B: S.53 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.53 Water bridges: B:S.53 SO4.11: 2 residues within 4Å: Chain B: P.15, D.16 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.16 SO4.12: 4 residues within 4Å: Chain B: G.68, G.69, A.70, Q.71 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.69, B:A.70, B:Q.71 SO4.14: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kimura, H. et al., BTZO-1, a cardioprotective agent, reveals that macrophage migration inhibitory factor regulates ARE-mediated gene expression. Chem. Biol. (2010)

Release Date

2016-04-20

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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