SMTL ID : 2oow.1

MIF Bound to a Fluorinated OXIM Derivative

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 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 SO4.7: 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 SO4.9: 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 SO4.10: 2 residues within 4Å: Chain C: G.65, K.66 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.66 Water bridges: C:I.67, C:I.67

2 x OX4: 3-FLUORO-4-HYDROXYBENZALDEHYDE O-(CYCLOHEXYLCARBONYL)OXIME(Non-covalent)(Covalent)

OX4.3: 12 residues within 4Å: Chain A: P.1, M.2, K.32, Y.36, H.62, S.63, I.64, M.101, V.106 Chain B: Y.95, N.97 Ligands: GOL.4 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:M.2, A:H.62, A:I.64, A:I.64, A:V.106, B:Y.95, B:Y.95 Hydrogen bonds: A:K.32, A:I.64 Salt bridges: A:K.32 OX4.11: 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 Ligands: GOL.12 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:M.2, C:K.32, C:H.62, C:I.64, C:V.106, A:Y.95, A:Y.95 Hydrogen bonds: C:P.1, C:I.64 Salt bridges: C:K.32

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: P.1, M.2, H.62, S.63, V.106 Chain B: Y.95, N.97 Ligands: OX4.3 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.62, A:I.64, B:N.97 GOL.5: 1 residues within 4Å: Chain A: A.114 2 PLIP interactions: 2 interactions with chain A Water bridges: A:F.113, A:A.114 GOL.6: 3 residues within 4Å: Chain A: D.92 Chain C: N.109 Ligands: IPA.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.92 GOL.8: 8 residues within 4Å: Chain B: P.1, M.2, H.62, S.63, I.64, M.101, V.106 Chain C: N.97 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:N.97, C:N.97, B:P.1, B:I.64 GOL.12: 9 residues within 4Å: Chain A: Y.95, N.97 Chain C: P.1, M.2, H.62, S.63, I.64, V.106 Ligands: OX4.11 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:P.1, C:H.62, C:I.64, A:N.97 GOL.13: 1 residues within 4Å: Chain C: A.114 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.114

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

IPA.14: 4 residues within 4Å: Chain C: Q.35, Y.36, W.108 Ligands: GOL.6 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:Y.36 Water bridges: A:D.92, A:D.92 IPA.15: 6 residues within 4Å: Chain C: D.16, G.17, F.18, L.19, S.20 Ligands: IPA.16 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.19, C:L.19 Hydrogen bonds: C:G.17, C:F.18 IPA.16: 5 residues within 4Å: Chain C: G.17, F.18, L.19, S.20 Ligands: IPA.15 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.19 Hydrogen bonds: C:G.17, C:G.17, C:L.19, C:S.20

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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