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Crystal structure of kkofab in complex with platelet factor 4

Analyse Crystal structure of kkofab in complex with platelet factor 4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4R9Y
Type: protein
Length: 1,124 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Platelet factor 4; Platelet factor 4 antibody kko light chain; Platelet factor 4 antibody…
UniProt: P02776
Pockets: 17 · best druggability 0.85

Structure

x-ray diffraction · 3 distinct chains · 4% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, C, B, A	Platelet factor 4	protein	65	14% helix, 18% strand	P02776
L, M	Platelet factor 4 antibody kko light chain	protein	214	6% helix, 41% strand	—
H, N	Platelet factor 4 antibody kko heavy chain	protein	218	0% helix, 41% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1000	0.85	0.85	96	empty
2	159	0.74	0.91	32	empty
3	592	0.65	0.75	75	empty
4	57	0.62	0.92	20	empty
5	400	0.57	0.74	49	empty

Interfaces

16 interfaces between chains.

L–H · 2013 Å² buried · 13 hydrogen bonds · protein-protein
M–N · 1973 Å² buried · 12 hydrogen bonds · protein-protein
D–C · 855 Å² buried · 8 hydrogen bonds · protein-protein
B–A · 833 Å² buried · 7 hydrogen bonds · protein-protein
D–B · 656 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 disulfide (disulfide).

Compared structures

4R9Y · Crystal structure of KKOFab in complex with platelet factor 4 · the same entry in another collection · chain N against N, TM-score 1.00
P02776 · AlphaFold monomer V2.0 prediction for platelet factor 4 (P02776) · a predicted model of the same protein · chain D against A, TM-score 0.81

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 P02776
Elsewhere: RCSB PDB 4R9Y · PDBe 4R9Y · UniProt P02776

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