SMTL ID : 4pkk.1

Crystal structure of Macrophage Migration inhibitory factor in complex with furan-2-ylmethyl)imino methanethiol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-trimer

Ligands

3 x 31E: (Z)-[(furan-2-ylmethyl)imino]methanethiol(Covalent)

31E.1: 11 residues within 4Å: Chain A: P.1, M.2, K.32, Y.36, H.62, S.63, I.64, M.101, V.106 Chain C: Y.95, N.97 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:V.106 Water bridges: A:I.64 pi-Stacking: C:Y.95 31E.7: 11 residues within 4Å: Chain A: Y.95, N.97 Chain B: P.1, M.2, Y.36, H.62, S.63, I.64, M.101, V.106 Ligands: IPA.12 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B pi-Stacking: A:Y.95 Hydrophobic interactions: B:V.106 Water bridges: B:I.64 31E.13: 10 residues within 4Å: Chain B: Y.95, N.97 Chain C: P.1, M.2, Y.36, H.62, S.63, I.64, M.101, V.106 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:V.106 Water bridges: C:I.64 pi-Stacking: B:Y.95

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: N.109, N.110 Ligands: GOL.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.109, A:N.109, A:N.110 GOL.3: 6 residues within 4Å: Chain A: N.109, N.110 Chain C: S.90, P.91, D.92 Ligands: GOL.2 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:D.92, A:N.110 GOL.4: 3 residues within 4Å: Chain A: G.65, K.66, Q.71 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.66, A:Q.71 Water bridges: A:I.67, A:I.67 GOL.8: 3 residues within 4Å: Chain B: G.65, K.66, Q.71 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.66, B:I.67, B:Q.71 Water bridges: B:I.67

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

SO4.5: 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 SO4.6: 5 residues within 4Å: Chain A: D.16, G.17, F.18, L.19, S.20 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.17, A:G.17, A:L.19, A:S.20 Water bridges: A:F.18, A:F.18 SO4.9: 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.69, B:A.70, B:Q.71, B:Q.71 Water bridges: B:I.67

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

IPA.10: 2 residues within 4Å: Chain B: P.15, D.16 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.15, B:D.16 Hydrogen bonds: B:D.16 IPA.11: 2 residues within 4Å: Chain B: A.70, R.73 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.70 Hydrogen bonds: B:R.73 IPA.12: 4 residues within 4Å: Chain A: Y.95 Chain B: Y.36, F.113 Ligands: 31E.7 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.113 IPA.14: 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

Pantouris, G. et al., Crystal structure of Macrophage Migration inhibitory factor with a covalent inhibitor. To Be Published

Release Date

2016-05-04

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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