SMTL ID : 7xtx.1

High resolution crystal structure of human macrophage migration inhibitory factor in complex with methotrexate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.28 Å

Oligo State

homo-trimer

Ligands

4 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 SO4.8: 5 residues within 4Å: Chain B: G.68, G.69, A.70, Q.71 Ligands: EDO.13 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.69, B:A.70, B:Q.71, B:Q.71 SO4.14: 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 SO4.15: 4 residues within 4Å: Chain C: G.17, F.18, L.19, S.20 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.17, C:L.19, C:S.20, C:S.20, C:S.20 Water bridges: C:F.18

11 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 4 residues within 4Å: Chain A: G.65, K.66, I.67, Q.71 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.66, A:I.67, A:Q.71 Water bridges: A:K.32 EDO.3: 1 residues within 4Å: Chain A: A.114 No protein-ligand interaction detected (PLIP) EDO.4: 4 residues within 4Å: Chain A: P.1, S.63, I.64 Chain B: Y.95 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.63, A:I.64 EDO.5: 6 residues within 4Å: Chain A: Y.95, N.97 Chain C: M.2, H.62, V.106 Ligands: EDO.17 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.97 Water bridges: A:Y.95 EDO.9: 6 residues within 4Å: Chain B: P.1, M.2, H.62 Chain C: Y.95, N.97 Ligands: MT1.7 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.97, C:N.97 EDO.10: 2 residues within 4Å: Chain B: Q.35 Ligands: MT1.7 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Y.36, B:Y.36 EDO.11: 3 residues within 4Å: Chain B: S.52, E.54, R.93 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.52, B:R.93 EDO.12: 3 residues within 4Å: Chain B: D.100, M.101, N.102 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.100, B:N.102 EDO.13: 3 residues within 4Å: Chain B: A.70, Q.71 Ligands: SO4.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.70 Water bridges: B:S.74 EDO.16: 5 residues within 4Å: Chain C: A.84, R.88, I.89, S.90, P.91 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.88, C:I.89 EDO.17: 6 residues within 4Å: Chain A: Y.95 Chain C: P.1, K.32, S.63, I.64 Ligands: EDO.5 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:P.1, C:K.32, C:S.63, C:I.64

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

IPA.6: 3 residues within 4Å: Chain A: Q.35, Y.36, W.108 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:D.92 Hydrophobic interactions: A:Y.36 IPA.18: 3 residues within 4Å: Chain C: Q.35, Y.36, W.108 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.36 IPA.19: 2 residues within 4Å: Chain C: A.70, R.73 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.70 Hydrogen bonds: C:R.73

1 x MT1: N-(4-{[(2,4-DIAMINOPTERIDIN-1-IUM-6-YL)METHYL](METHYL)AMINO}BENZOYL)-L-GLUTAMIC ACID(Non-covalent)

MT1.7: 11 residues within 4Å: Chain B: P.1, K.32, Q.35, Y.36, I.64, W.108, F.113 Chain C: F.49, Y.95 Ligands: EDO.9, EDO.10 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:Q.35, B:Y.36 Water bridges: B:K.32, B:I.64, B:I.64 pi-Stacking: B:Y.36 pi-Cation interactions: B:F.113 Hydrogen bonds: C:Y.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sugishima, K. et al., Identification of methotrexate as an inhibitor of macrophage migration inhibitory factor by high-resolution crystal structure analysis. To Be Published

Release Date

2023-05-24

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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