SMTL ID : 5xej.1

Crystal Structure of Macrophage Migration Inhibitory Factor bound to MTX

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-trimer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: P.15, D.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.16 SO4.2: 5 residues within 4Å: Chain A: D.16, G.17, F.18, L.19, S.20 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.17, A:G.17, A:L.19, A:S.20 SO4.3: 6 residues within 4Å: Chain A: V.42, Q.45 Chain B: V.42, Q.45 Chain C: V.42, Q.45 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: B:Q.45, C:Q.45, A:Q.45 SO4.5: 6 residues within 4Å: Chain A: H.62, Y.99 Chain B: H.62, Y.99 Chain C: H.62, Y.99 6 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: B:Y.99 Water bridges: B:Y.99, A:Y.99 Salt bridges: B:H.62, A:H.62, C:H.62

1 x 6UV: (2~{R})-2-[[4-[[2,4-bis(azanyl)pteridin-6-yl]methyl-methyl-amino]phenyl]carbonylamino]pentanedioic acid(Non-covalent)

6UV.4: 13 residues within 4Å: Chain A: P.1, M.2, K.32, P.33, Y.36, H.62, S.63, I.64, K.66, V.106, F.113 Chain C: Y.95, N.97 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:K.32, A:Y.36, A:I.64, C:Y.95 Hydrogen bonds: A:I.64, A:K.66, C:Y.95, C:N.97 Salt bridges: A:K.32 pi-Cation interactions: A:K.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fukushima, K. et al., Structure of macrophage migration inhibitory factor in complex with methotrexate. Acta Crystallogr D Struct Biol (2021)

Release Date

2018-07-25

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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