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Crystal structure of STH1 bromodomain

Analyse Crystal structure of STH1 bromodomain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6KMB
Type: protein
Length: 435 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nuclear protein STH1/NPS1
EC: 3.6.4.12
UniProt: P32597
Pockets: 5 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 60% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nuclear protein STH1/NPS1 (EC 3.6.4.12)	protein	110	57% helix, 2% strand	P32597
B	Nuclear protein STH1/NPS1 (EC 3.6.4.12)	protein	109	60% helix, 2% strand	P32597
C	Nuclear protein STH1/NPS1 (EC 3.6.4.12)	protein	108	62% helix, 2% strand	P32597
D	Nuclear protein STH1/NPS1 (EC 3.6.4.12)	protein	108	61% helix, 2% strand	P32597

Ligands and binding sites

GOL · Glycerol · additive · 3 copies · chains B, D, A, C

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	309	0.84	0.94	47	GOL
2	289	0.84	0.95	46	GOL
3	84	0.34	0.75	16	empty
4	70	0.31	0.74	14	empty
5	69	0.29	0.73	14	empty

Interfaces

6 interfaces between chains.

B–D · 1005 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 961 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 297 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 280 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 189 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6KMB · Crystal structure of Sth1 bromodomain · the same entry in another collection · chain D against D, TM-score 1.00
P32597 · AlphaFold monomer V2.0 prediction for nuclear protein STH1/NPS1 (P32597) · a predicted model of the same protein · chain D against A, TM-score 0.97

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 P32597
Elsewhere: RCSB PDB 6KMB · PDBe 6KMB · UniProt P32597

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