Research workbench

DHD15_EXTENDED

Analyse DHD15_EXTENDED in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6DM9
Type: protein
Length: 305 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DHD15_EXTENDED_A; DHD15_EXTENDED_B
Ligands: SO4
Pockets: 2 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 96% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	DHD15_EXTENDED_A	protein	78	95% helix, 0% strand	—
B	DHD15_EXTENDED_B	protein	75	97% helix, 0% strand	—
D	DHD15_EXTENDED_B	protein	74	96% helix, 0% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 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	324	0.78	0.89	40	empty
2	106	0.58	0.86	28	empty

Interfaces

6 interfaces between chains.

C–D · 1868 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 1836 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 1697 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 1383 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 272 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (formylation).

Compared structures

6DM9 · DHD15_extended · 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
Elsewhere: RCSB PDB 6DM9 · PDBe 6DM9

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