MolNFT v1 · #154500 · protein

Shuguo pwwp domain

6KD6 · LD23804P: “Shuguo pwwp domain”. X-ray diffraction, 4 pockets (best druggability 0.69). MolNFT v1 #154500 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6KD6
Type: protein
Length: 325 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: LD23804P
UniProt: Q9VAA9
Pockets: 4 · best druggability 0.69

Structure

x-ray diffraction · 4 distinct chains · 41% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	LD23804P	protein	80	39% helix, 34% strand	Q9VAA9
B	LD23804P	protein	84	40% helix, 32% strand	Q9VAA9
C	LD23804P	protein	81	41% helix, 33% strand	Q9VAA9
D	LD23804P	protein	80	43% helix, 33% strand	Q9VAA9

Pockets

4 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	231	0.69	0.85	37	empty
2	161	0.67	0.87	30	empty
3	516	0.63	0.75	37	empty
4	168	0.45	0.75	21	empty

Interfaces

5 interfaces between chains.

A–B · 1564 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 1493 Å² buried · 18 hydrogen bonds · protein-protein
B–D · 261 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 89 Å² buried · 1 hydrogen bond · protein-protein
A–C · 61 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6KD6 · Shuguo PWWP domain · 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 Q9VAA9
Elsewhere: RCSB PDB 6KD6 · PDBe 6KD6 · UniProt Q9VAA9

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