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A novel structure-based mechanism for DNA-binding of SATB1

Analyse A novel structure-based mechanism for DNA-binding of SATB1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4Q2J
Type: protein
Length: 524 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-binding protein SATB1
UniProt: Q60611
Pockets: 4 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 34% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-binding protein SATB1	protein	169	40% helix, 20% strand	Q60611
B	DNA-binding protein SATB1	protein	94	32% helix, 37% strand	Q60611
C	DNA-binding protein SATB1	protein	92	16% helix, 38% strand	Q60611
D	DNA-binding protein SATB1	protein	169	40% helix, 21% strand	Q60611

Pockets

4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1063	0.75	0.78	90	empty
2	55	0.32	0.77	18	empty
3	51	0.30	0.76	18	empty
4	56	0.27	0.74	15	empty

Interfaces

4 interfaces between chains.

A–B · 795 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 652 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 549 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 496 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

4Q2J · A novel structure-based mechanism for DNA-binding of SATB1 · the same entry in another collection · chain D against D, TM-score 1.00
Q60611 · AlphaFold monomer V2.0 prediction for DNA-binding protein SATB1 (Q60611) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 Q60611
Elsewhere: RCSB PDB 4Q2J · PDBe 4Q2J · UniProt Q60611

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