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Crystal structure of PDSP15A

Analyse Crystal structure of PDSP15A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4OZD
Type: protein
Length: 840 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 14.4 kda salivary protein
UniProt: Q06KA5
Pockets: 10 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 68% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G	14.4 kda salivary protein	protein	120	68% helix, 0% strand	Q06KA5

Pockets

10 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	1086	0.80	0.81	111	empty
2	659	0.71	0.78	63	empty
3	458	0.68	0.79	52	empty
4	214	0.50	0.75	29	empty
5	128	0.45	0.77	21	empty

Interfaces

9 interfaces between chains.

B–C · 930 Å² buried · 16 hydrogen bonds · protein-protein
A–D · 876 Å² buried · 11 hydrogen bonds · protein-protein
D–F · 855 Å² buried · 7 hydrogen bonds · protein-protein
F–G · 807 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 254 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 21 disulfide (disulfide).

Compared structures

4OZD · Crystal structure of PdSP15a · the same entry in another collection · chain A against A, 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 Q06KA5
Elsewhere: RCSB PDB 4OZD · PDBe 4OZD · UniProt Q06KA5

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