SMTL ID : 9jit.1

Macrophage migration inhibitory factor S61H/Y100H mutant (MIF(S61H/Y100H))

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.08 Å

Oligo State

homo-trimer

Ligands

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

SO4.1: 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: 4 residues within 4Å: Chain B: G.69, G.70, A.71, Q.72 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.71, B:Q.72, B:Q.72 Water bridges: B:G.70, B:G.70 SO4.5: 6 residues within 4Å: Chain A: H.61, H.63 Chain B: H.61, H.63 Chain C: H.61, H.63 8 PLIP interactions: 2 interactions with chain C, 4 interactions with chain A, 2 interactions with chain B Salt bridges: C:H.61, C:H.63, A:H.61, A:H.63, B:H.61, B:H.63 Water bridges: A:H.61, A:H.61 SO4.8: 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.2: 9 residues within 4Å: Chain A: P.2, M.3, Y.37, H.63, S.64, I.65, V.107 Chain B: Y.96, N.98 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:P.2, A:M.3, A:H.63, A:I.65, B:N.98, B:N.98 Water bridges: A:P.2, B:Y.96, B:Y.96 GOL.6: 9 residues within 4Å: Chain B: P.2, M.3, H.63, S.64, I.65, M.102, V.107 Chain C: N.98 Ligands: IPA.7 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:P.2, B:H.63, B:I.65, C:N.98, C:N.98 GOL.9: 9 residues within 4Å: Chain A: Y.96, N.98 Chain C: P.2, M.3, Y.37, H.63, S.64, I.65, V.107 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:P.2, C:M.3, C:I.65, A:N.98, A:N.98 Water bridges: A:Y.96

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

IPA.3: 3 residues within 4Å: Chain A: Q.36, Y.37, W.109 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.37, A:W.109 Hydrogen bonds: A:Y.37 IPA.7: 4 residues within 4Å: Chain B: K.33, I.65, F.114 Ligands: GOL.6 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.65, B:F.114 Water bridges: B:K.33 IPA.10: 3 residues within 4Å: Chain C: Q.36, Y.37, W.109 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:Y.37 Water bridges: A:D.93, A:D.93, 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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