SMTL ID : 2ooz.1

Macrophage Migration Inhibitory Factor (MIF) Complexed with OXIM6 (an OXIM Derivative Not Containing a Ring in its R-group)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-trimer

Ligands

5 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 SO4.2: 2 residues within 4Å: Chain A: G.65, K.66 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.66 Water bridges: A:I.67 SO4.6: 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 SO4.7: 2 residues within 4Å: Chain B: G.65, K.66 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.66 Water bridges: B:I.67, B:Q.71 SO4.10: 4 residues within 4Å: Chain C: G.68, G.69, A.70, Q.71 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:A.70, C:Q.71, C:Q.71 Water bridges: C:G.69, C:G.69

2 x OX5: 4-HYDROXYBENZALDEHYDE O-(3,3-DIMETHYLBUTANOYL)OXIME(Non-covalent)

OX5.3: 11 residues within 4Å: Chain A: P.1, M.2, Y.36, H.62, S.63, I.64, M.101, V.106, F.113 Chain B: Y.95, N.97 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:N.97, A:P.1 pi-Stacking: B:Y.95 Hydrophobic interactions: A:H.62, A:I.64, A:V.106 OX5.8: 11 residues within 4Å: Chain B: P.1, M.2, Y.36, H.62, S.63, I.64, M.101, V.106, F.113 Chain C: Y.95, N.97 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:N.97 pi-Stacking: C:Y.95 Hydrophobic interactions: B:H.62, B:I.64, B:V.106

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 1 residues within 4Å: Chain A: A.114 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.114, A:A.114 GOL.9: 1 residues within 4Å: Chain B: A.114 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.114 GOL.11: 8 residues within 4Å: Chain A: N.97 Chain C: P.1, M.2, H.62, S.63, I.64, M.101, V.106 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:H.62, C:I.64, A:N.97, A:N.97 Water bridges: C:P.1

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

IPA.5: 3 residues within 4Å: Chain A: Q.35, Y.36, W.108 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.36, A:W.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Crichlow, G.V. et al., Alternative chemical modifications reverse the binding orientation of a pharmacophore scaffold in the active site of macrophage migration inhibitory factor. J.Biol.Chem. (2007)

Release Date

2007-06-05

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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