SMTL ID : 9jiz.1

Macrophage migration inhibitory factor S61H/Y100H mutant complexed with three Zinc ions (Zn3-MIF(S61H/Y100H))

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-trimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.61, H.100 Chain C: H.63 Ligands: CO3.2 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Metal complexes: A:H.61, A:H.100, C:H.63 ZN.7: 4 residues within 4Å: Chain A: H.63 Chain B: H.61, H.100 Ligands: CO3.2 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Metal complexes: A:H.63, B:H.61, B:H.100 ZN.11: 4 residues within 4Å: Chain B: H.63 Chain C: H.61, H.100 Ligands: CO3.2 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Metal complexes: C:H.61, C:H.100, B:H.63

1 x CO3: CARBONATE ION(Non-functional Binders)

CO3.2: 12 residues within 4Å: Chain A: H.61, H.63, H.100 Chain B: H.61, H.63, H.100 Chain C: H.61, H.63, H.100 Ligands: ZN.1, ZN.7, ZN.11 No protein-ligand interaction detected (PLIP)

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

SO4.3: 4 residues within 4Å: Chain A: G.69, G.70, A.71, Q.72 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.69, A:G.70, A:A.71, A:Q.72, A:Q.72 SO4.4: 2 residues within 4Å: Chain A: G.66, K.67 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.67 Water bridges: A:K.33, A:I.68, A:I.68, A:Q.72 Salt bridges: A:K.67 SO4.8: 4 residues within 4Å: Chain B: G.69, G.70, A.71, Q.72 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.70, B:A.71, B:Q.72, B:Q.72 SO4.12: 4 residues within 4Å: Chain C: G.69, G.70, A.71, Q.72 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.70, C:A.71, C:Q.72, C:Q.72

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: P.2, S.64, I.65, F.114 Chain B: Y.96 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.64, A:I.65, B:Y.96 GOL.9: 9 residues within 4Å: Chain B: P.2, M.3, H.63, S.64, I.65, V.107 Chain C: Y.96, N.98 Ligands: IPA.10 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:N.98, C:N.98, B:I.65 GOL.13: 7 residues within 4Å: Chain A: Y.96 Chain C: P.2, M.3, Y.37, H.63, S.64, I.65 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:Y.96, C:P.2, C:I.65

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

IPA.6: 3 residues within 4Å: Chain A: Q.36, Y.37, W.109 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.37 Hydrogen bonds: A:Y.37 IPA.10: 7 residues within 4Å: Chain B: P.2, K.33, Y.37, I.65, F.114 Chain C: Y.96 Ligands: GOL.9 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:K.33, B:Y.37, B:I.65, B:F.114 Hydrogen bonds: B:K.33 IPA.14: 3 residues within 4Å: Chain C: Q.36, Y.37, W.109 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:Y.37, C:W.109 Water bridges: A:D.93, A:D.93 IPA.15: 2 residues within 4Å: Chain C: K.33, I.65 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:K.33, C:I.65 Hydrogen bonds: C:K.33 Water bridges: C:K.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ueno, A. et al., A cytokine-based designer enzyme with an abiological multinuclear metal center exhibits intrinsic and extrinsic catalysis. Nat Commun (2025)

Release Date

2025-08-06

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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