MolNFT v1 · #5953 · protein

Structure of stem cell factor

1EXZ: “Structure of stem cell factor”. X-ray diffraction, 2 ligands (SM, CA), 6 pockets (best druggability 0.73). MolNFT v1 #5953 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1EXZ
Type: protein
Length: 528 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Stem cell factor
UniProt: P21583
Ligands: SM, CA
Pockets: 6 · best druggability 0.73

Structure

x-ray diffraction · 4 distinct chains · 46% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Stem cell factor	protein	133	49% helix, 8% strand	P21583
B	Stem cell factor	protein	140	42% helix, 6% strand	P21583
C	Stem cell factor	protein	131	44% helix, 6% strand	P21583
D	Stem cell factor	protein	124	48% helix, 6% strand	P21583

Ligands and binding sites

SM · Samarium (III) ion · metal · 4 copies · chains B, D, C, A
CA · Calcium ion · metal · 2 copies · chains A, B, C
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B, D

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

Pockets

6 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	557	0.73	0.81	65	empty
2	185	0.48	0.76	37	CA
3	95	0.41	0.77	18	empty
4	134	0.39	0.74	22	empty
5	60	0.35	0.78	16	empty

Interfaces

5 interfaces between chains.

C–D · 888 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 798 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 438 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 419 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 364 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

1EXZ · Structure of 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 0.89

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 1EXZ · PDBe 1EXZ · UniProt P21583

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