MolNFT v1 · #156035 · protein

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

6LR3: “Structural and functional insights into macrophage migration inhibitory factor from oncomelania hupensis, the…”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.83). MolNFT v1 #156035 on GenesisL1: 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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