SMTL ID : 7kqx.1

MIF Y99C homotrimeric mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-trimer

Ligands

3 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 SO4.10: 4 residues within 4Å: Chain B: G.68, G.69, A.70, Q.71 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.68, B:G.69, B:A.70, B:Q.71, B:Q.71 SO4.18: 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

15 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: P.1, M.2, H.62, S.63, I.64, V.106 Chain C: Y.95, N.97 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:N.97, C:N.97, A:P.1, A:P.1, A:M.2, A:I.64 GOL.3: 1 residues within 4Å: Chain A: E.54 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.54 GOL.4: 9 residues within 4Å: Chain A: Y.95, N.97 Chain B: P.1, M.2, Y.36, H.62, S.63, I.64, V.106 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.62, B:I.64, A:N.97, A:N.97 GOL.5: 8 residues within 4Å: Chain A: L.58, C.59, S.60, N.97 Chain B: M.2, I.4, H.62 Ligands: IPA.9 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.58, A:N.97, B:H.62 Water bridges: A:S.60 GOL.11: 4 residues within 4Å: Chain B: G.51, S.53 Chain C: L.19, S.20 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.53, B:S.53 Water bridges: B:S.53 GOL.12: 2 residues within 4Å: Chain B: G.65, K.66 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.66 Water bridges: B:I.67, B:Q.71, B:D.100 GOL.13: 4 residues within 4Å: Chain B: G.50, S.52, R.93 Chain C: Q.35 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.52, B:R.93 Water bridges: B:F.49 GOL.14: 8 residues within 4Å: Chain B: L.58, C.59, S.60, N.97 Chain C: M.2, I.4, H.62 Ligands: IPA.9 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:L.58, B:N.97, C:H.62 Water bridges: B:S.60 GOL.15: 3 residues within 4Å: Chain B: W.108, T.112, A.114 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.112, B:A.114 Water bridges: B:S.111, B:T.112 GOL.16: 3 residues within 4Å: Chain B: D.92 Chain C: W.108, N.109 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.109 GOL.19: 6 residues within 4Å: Chain C: P.15, D.16, G.17, F.18, E.21, R.86 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.17, C:E.21 Water bridges: C:D.16 GOL.20: 9 residues within 4Å: Chain B: Y.95, N.97 Chain C: P.1, M.2, H.62, S.63, I.64, M.101, V.106 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:P.1, C:I.64, B:N.97, B:N.97 GOL.21: 9 residues within 4Å: Chain A: M.2, I.4, H.62 Chain C: N.6, L.58, C.59, S.60, N.97 Ligands: IPA.9 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:S.60, C:N.97, A:H.62 Water bridges: C:S.60 GOL.22: 5 residues within 4Å: Chain A: Q.35 Chain C: F.49, G.50, S.52, R.93 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Water bridges: C:S.52, C:R.93, A:Q.35 GOL.23: 4 residues within 4Å: Chain C: G.17, S.20, E.21, Q.24 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.20, C:S.20, C:Q.24

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

IPA.6: 4 residues within 4Å: Chain A: H.62 Chain B: H.62 Chain C: H.62 Ligands: IPA.9 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.62 IPA.7: 3 residues within 4Å: Chain A: Q.35, Y.36, W.108 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.108 Hydrogen bonds: A:Y.36 IPA.8: 4 residues within 4Å: Chain A: G.17, S.20, E.21, Q.24 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.21 Hydrogen bonds: A:Q.24 IPA.9: 8 residues within 4Å: Chain A: I.4, S.60 Chain B: I.4, S.60 Ligands: GOL.5, IPA.6, GOL.14, GOL.21 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 3 interactions with chain A Water bridges: C:S.60, B:S.60, A:S.60, A:H.62 Hydrophobic interactions: A:I.4 IPA.17: 3 residues within 4Å: Chain B: Q.35, Y.36, W.108 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:D.92, A:D.92 Hydrophobic interactions: B:Y.36, B:W.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Skeens, E. et al., A Cysteine Variant at an Allosteric Site Alters MIF Dynamics and Biological Function in Homo- and Heterotrimeric Assemblies. Front Mol Biosci (2022)

Release Date

2022-01-19

Peptides

Macrophage migration inhibitory factor: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Macrophage migration inhibitory factor