MolNFT v1 · #182669 · protein

Structure of human leukaemia inhibitory factor with Fab MSC1

7N0A · Leukemia inhibitory factor: “Structure of human leukaemia inhibitory factor with Fab MSC1”. X-ray diffraction, 2 ligands (NAG, BMA), 7 pockets (best druggability 0.62). MolNFT v1 #182669 on GenesisL1: 3D structure, binding sites and…

PDB: 7N0A
Type: protein
Length: 611 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Leukemia inhibitory factor; Msc-1 Fab light chain; Msc-1 Fab heavy chain
UniProt: P15018
Ligands: NAG, BMA
Pockets: 7 · best druggability 0.62

Structure

x-ray diffraction · 3 distinct chains · 20% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Leukemia inhibitory factor	protein	172	63% helix, 0% strand	P15018
A	Msc-1 Fab light chain	protein	219	2% helix, 47% strand	—
B	Msc-1 Fab heavy chain	protein	220	5% helix, 52% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains C
BMA · beta-D-mannopyranose · sugar · chains C
GOL · Glycerol · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	625	0.62	0.74	56	empty
2	68	0.52	0.86	18	empty
3	70	0.52	0.85	16	empty
4	156	0.50	0.78	29	empty
5	122	0.42	0.76	28	empty

Interfaces

3 interfaces between chains.

A–B · 1768 Å² buried · 13 hydrogen bonds · protein-protein
C–B · 771 Å² buried · 11 hydrogen bonds · protein-protein
C–A · 402 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

7N0A · Structure of Human Leukaemia Inhibitory Factor with Fab MSC1 · the same entry in another collection · chain C against C, TM-score 1.00
P15018 · AlphaFold monomer V2.0 prediction for leukemia inhibitory factor (P15018) · a predicted model of the same protein · chain C against A, TM-score 0.95

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 P15018
Elsewhere: RCSB PDB 7N0A · PDBe 7N0A · UniProt P15018

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