MolNFT v1 · #180215 · protein + DNA

Crystal structure of HSAMD9_DBD with DNA

7KSP · Sterile alpha motif domain-containing protein 9: “Crystal structure of HSAMD9_DBD with DNA”. X-ray diffraction, 4 pockets (best druggability 0.83). MolNFT v1 #180215 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7KSP
Type: protein + DNA
Length: 468 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sterile alpha motif domain-containing protein 9; DNA
UniProt: Q5K651
Pockets: 4 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 35% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sterile alpha motif domain-containing protein 9	protein	212	33% helix, 22% strand	Q5K651
B	Sterile alpha motif domain-containing protein 9	protein	212	36% helix, 21% strand	Q5K651
C	DNA	dna	22	—	—
D	DNA	dna	22	—	—

Pockets

4 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	1170	0.83	0.84	90	empty
2	480	0.61	0.76	44	empty
3	200	0.45	0.74	42	empty
4	70	0.35	0.76	13	empty

Interfaces

5 interfaces between chains.

C–D · 978 Å² buried · 76 hydrogen bonds · nucleic-nucleic
A–C · 265 Å² buried · 1 hydrogen bond · protein-nucleic
B–D · 186 Å² buried · 1 hydrogen bond · protein-nucleic
B–C · 157 Å² buried · 3 hydrogen bonds · protein-nucleic
A–D · 142 Å² buried · 1 hydrogen bond · protein-nucleic

Compared structures

7KSP · Crystal structure of hSAMD9_DBD with DNA · the same entry in another collection · chain A against A, TM-score 1.00
Q5K651 · AlphaFold monomer V2.0 prediction for sterile alpha motif domain- containing protein 9… · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q5K651
Elsewhere: RCSB PDB 7KSP · PDBe 7KSP · UniProt Q5K651

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