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Crystal structure of the human colony-stimulating factor 1 (hcsf-1) cytokine in complex with the viral receptor BARF1

Analyse Crystal structure of the human colony-stimulating factor 1 (hcsf-1) cytokine in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ADF
Type: protein
Length: 3,950 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Secreted protein BARF1; Macrophage colony-stimulating factor 1
UniProt: P0CW72, P09603
Ligands: MAN, NAG, BMA
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 20 distinct chains · 24% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Secreted protein BARF1	protein	188	2% helix, 60% strand	P0CW72
B, P	Secreted protein BARF1	protein	189	2% helix, 60% strand	P0CW72
C	Secreted protein BARF1	protein	186	2% helix, 60% strand	P0CW72
D	Secreted protein BARF1	protein	187	2% helix, 60% strand	P0CW72
E	Secreted protein BARF1	protein	187	2% helix, 59% strand	P0CW72
F	Secreted protein BARF1	protein	189	2% helix, 60% strand	P0CW72
G	Macrophage colony-stimulating factor 1	protein	145	60% helix, 8% strand	P09603
H, J, T	Macrophage colony-stimulating factor 1	protein	142	61% helix, 8% strand	P09603
I	Macrophage colony-stimulating factor 1	protein	137	59% helix, 9% strand	P09603
K	Macrophage colony-stimulating factor 1	protein	143	61% helix, 8% strand	P09603
L	Macrophage colony-stimulating factor 1	protein	135	60% helix, 9% strand	P09603
M	Secreted protein BARF1	protein	191	2% helix, 59% strand	P0CW72
N	Secreted protein BARF1	protein	191	2% helix, 60% strand	P0CW72
O	Secreted protein BARF1	protein	186	2% helix, 60% strand	P0CW72
Q	Secreted protein BARF1	protein	185	2% helix, 60% strand	P0CW72
R	Secreted protein BARF1	protein	186	2% helix, 60% strand	P0CW72
S, U	Macrophage colony-stimulating factor 1	protein	144	60% helix, 8% strand	P09603
V	Macrophage colony-stimulating factor 1	protein	141	60% helix, 9% strand	P09603
W	Macrophage colony-stimulating factor 1	protein	142	57% helix, 8% strand	P09603
X	Macrophage colony-stimulating factor 1	protein	139	60% helix, 9% strand	P09603

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 36 copies · chains C, N
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, B, C, D, E, F, M, N, O, P, Q, R
BMA · beta-D-mannopyranose · sugar · 12 copies

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1035	0.82	0.83	101	empty
2	340	0.58	0.76	36	empty
3	253	0.58	0.78	34	empty
4	296	0.58	0.77	31	empty
5	275	0.57	0.77	31	empty

Interfaces

58 interfaces between chains.

A–D · 1515 Å² buried · 35 hydrogen bonds · protein-protein
P–Q · 1505 Å² buried · 30 hydrogen bonds · protein-protein
N–R · 1499 Å² buried · 33 hydrogen bonds · protein-protein
B–F · 1469 Å² buried · 28 hydrogen bonds · protein-protein
M–O · 1445 Å² buried · 32 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 54 disulfide, 12 glycan (disulfide, N-glycosylation).

Compared structures

4ADF · CRYSTAL STRUCTURE OF THE HUMAN COLONY-STIMULATING FACTOR 1 (hCSF-1) CYTOKINE IN COMPLEX… · the same entry in another collection · chain I against I, 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 P0CW72
Every structure of UniProt P09603
Elsewhere: RCSB PDB 4ADF · PDBe 4ADF · UniProt P0CW72 · UniProt P09603

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