Research workbench

Human recombinant stem cell factor

Analyse Human recombinant stem cell factor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1SCF
Type: protein
Length: 448 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Stem cell factor
UniProt: P21583
Ligands: CA
Pockets: 2 · best druggability 0.63

Structure

x-ray diffraction · 4 distinct chains · 55% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Stem cell factor	protein	119	50% helix, 7% strand	P21583
B	Stem cell factor	protein	121	54% helix, 7% strand	P21583
C	Stem cell factor	protein	104	59% helix, 8% strand	P21583
D	Stem cell factor	protein	104	59% helix, 8% strand	P21583

Ligands and binding sites

CA · Calcium ion · metal · 3 copies · chains C, D
1PE · Pentaethylene glycol · additive · chains B, D

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	490	0.63	0.76	47	empty
2	395	0.61	0.76	28	1PE

Interfaces

4 interfaces between chains.

C–D · 856 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 854 Å² buried · 14 hydrogen bonds · protein-protein
B–D · 289 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 154 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified, 2 disulfide (engineered, disulfide).

Compared structures

1SCF · Human recombinant stem cell factor · the same entry in another collection · chain D against D, TM-score 1.00
P21583 · AlphaFold monomer V2.0 prediction for kit ligand (P21583) · a predicted model of the same protein · chain D against A, TM-score 0.92

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 P21583
Elsewhere: RCSB PDB 1SCF · PDBe 1SCF · UniProt P21583

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