SMTL ID : 9jj0.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-trimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.63 Chain B: H.100 Ligands: CO3.4, CL.9 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.63, B:H.100 ZN.2: 4 residues within 4Å: Chain A: H.100 Chain C: H.63 Ligands: CL.3, CO3.4 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Metal complexes: C:H.63, A:H.100 ZN.8: 4 residues within 4Å: Chain B: H.63 Chain C: H.100 Ligands: CO3.4, CL.13 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Metal complexes: C:H.100, B:H.63

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 6 residues within 4Å: Chain A: S.61, N.98, H.100 Chain C: H.63 Ligands: ZN.2, CO3.4 Ligand excluded by PLIP CL.9: 6 residues within 4Å: Chain A: H.63 Chain B: S.61, N.98, H.100 Ligands: ZN.1, CO3.4 Ligand excluded by PLIP CL.13: 6 residues within 4Å: Chain B: H.63 Chain C: S.61, N.98, H.100 Ligands: CO3.4, ZN.8 Ligand excluded by PLIP

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

CO3.4: 12 residues within 4Å: Chain A: H.63, H.100 Chain B: H.63, H.100 Chain C: H.63, H.100 Ligands: ZN.1, ZN.2, CL.3, ZN.8, CL.9, CL.13 No protein-ligand interaction detected (PLIP)

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

SO4.5: 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 SO4.10: 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 SO4.14: 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.6: 7 residues within 4Å: Chain A: P.2, M.3, H.63, S.64, V.107 Chain B: Y.96, N.98 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:M.3, A:H.63, B:N.98, B:N.98 GOL.11: 8 residues within 4Å: Chain B: P.2, M.3, H.63, S.64, I.65, V.107 Chain C: Y.96, N.98 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.15: 8 residues within 4Å: Chain A: Y.96, N.98 Chain C: P.2, M.3, H.63, S.64, I.65, V.107 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:N.98, A:N.98, C:P.2, C:P.2, C:I.65 Water bridges: A:Y.96, A:Y.96

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

IPA.7: 3 residues within 4Å: Chain A: Q.36, Y.37, W.109 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.109 Hydrogen bonds: A:Y.37 IPA.12: 4 residues within 4Å: Chain B: Y.37, W.109, T.113, F.114 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.109, B:F.114 Hydrogen bonds: B:F.114 IPA.16: 3 residues within 4Å: Chain C: Q.36, Y.37, W.109 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:Y.37 Water bridges: A:D.93

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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