MolNFT v1 · #155864 · protein

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

6LKV: “Structural and functional insights into macrophage migration inhibitory factor from oncomelania hupensis, the…”. X-ray diffraction, 2 ligands (CL, SO4), 3 pockets (best druggability 0.82). MolNFT v1 #155864 on GenesisL1: 3D…

PDB: 6LKV
Type: protein
Length: 557 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Macrophage migration inhibitory factor
UniProt: A0A1U9W5E8
Ligands: CL, SO4
Pockets: 3 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 45% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
F	Macrophage migration inhibitory factor	protein	141	44% helix, 23% strand	A0A1U9W5E8
A	Macrophage migration inhibitory factor	protein	138	46% helix, 24% strand	A0A1U9W5E8
B	Macrophage migration inhibitory factor	protein	140	45% helix, 24% strand	A0A1U9W5E8
C	Macrophage migration inhibitory factor	protein	138	46% helix, 21% strand	A0A1U9W5E8

Ligands and binding sites

CL · Chloride ion · ion · 2 copies · chains F, A, B, C
SO4 · Sulfate ion · ion · chains B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	199	0.82	0.96	28	CL
2	208	0.50	0.77	27	empty
3	78	0.33	0.74	17	empty

Interfaces

4 interfaces between chains.

F–A · 1198 Å² buried · 22 hydrogen bonds · protein-protein
F–B · 1186 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 1185 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 28 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6LKV · Structural and functional insights into macrophage migration inhibitory factor from… · the same entry in another collection · chain F against F, 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 6LKV · PDBe 6LKV · UniProt A0A1U9W5E8

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