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PHF20L1 TUDOR1 - mes

Analyse PHF20L1 TUDOR1 - mes in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6L10
Type: protein
Length: 275 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phd finger protein 20-like protein 1
UniProt: A8MW92
Ligands: SO4
Pockets: 5 · best druggability 0.61

Structure

x-ray diffraction · 3 distinct chains · 4% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Phd finger protein 20-like protein 1	protein	70	4% helix, 40% strand	A8MW92
C	Phd finger protein 20-like protein 1	protein	67	4% helix, 46% strand	A8MW92
D	Phd finger protein 20-like protein 1	protein	68	4% helix, 40% strand	A8MW92

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A, B, D, C
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 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	106	0.61	0.87	24	SO4
2	253	0.59	0.79	45	SO4, MES
3	61	0.44	0.82	10	MES
4	73	0.30	0.74	17	empty
5	66	0.29	0.73	19	empty

Interfaces

5 interfaces between chains.

A–D · 365 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 299 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 294 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 275 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 230 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6L10 · PHF20L1 Tudor1 - MES · the same entry in another collection · chain A against A, TM-score 1.00
A8MW92 · AlphaFold monomer V2.0 prediction for phd finger protein 20-like protein 1 (A8MW92) · a predicted model of the same protein · chain D against A, TM-score 0.94

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 A8MW92
Elsewhere: RCSB PDB 6L10 · PDBe 6L10 · UniProt A8MW92

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