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Structural and functional insights into macrophage migration inhibitory factor from oncomelania hupensis, the intermediate host of schistosoma japonicum

Analyse Structural and functional insights into macrophage migration inhibitory factor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6LR3
Type: protein
Length: 1,387 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Macrophage migration inhibitory factor
UniProt: A0A1U9W5E8
Ligands: SO4
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 6 distinct chains · 38% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Macrophage migration inhibitory factor	protein	116	38% helix, 29% strand	A0A1U9W5E8
C	Macrophage migration inhibitory factor	protein	118	37% helix, 29% strand	A0A1U9W5E8
D, F, L	Macrophage migration inhibitory factor	protein	115	38% helix, 30% strand	A0A1U9W5E8
B, G, J	Macrophage migration inhibitory factor	protein	117	38% helix, 29% strand	A0A1U9W5E8
H, K	Macrophage migration inhibitory factor	protein	114	39% helix, 30% strand	A0A1U9W5E8
I	Macrophage migration inhibitory factor	protein	113	39% helix, 30% strand	A0A1U9W5E8

Ligands and binding sites

SO4 · Sulfate ion · ion · 8 copies · chains A, C, D, B, E, F, G, H, I, J, K, L

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	229	0.83	0.96	30	SO4
2	226	0.82	0.96	29	SO4
3	226	0.82	0.95	30	SO4
4	271	0.79	0.91	42	SO4
5	967	0.76	0.78	95	empty

Interfaces

29 interfaces between chains.

K–L · 1205 Å² buried · 24 hydrogen bonds · protein-protein
H–I · 1186 Å² buried · 25 hydrogen bonds · protein-protein
C–D · 1186 Å² buried · 23 hydrogen bonds · protein-protein
E–F · 1178 Å² buried · 23 hydrogen bonds · protein-protein
G–I · 1175 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

6LR3 · Structural and functional insights into macrophage migration inhibitory factor from… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt A0A1U9W5E8
Elsewhere: RCSB PDB 6LR3 · PDBe 6LR3 · UniProt A0A1U9W5E8

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