MolNFT v1 · #174400 · protein

Crystal structure of SPINDLIN1-H3(K4ME3-K9ME2) complex

7BU9 · Spindlin-1: “Crystal structure of SPINDLIN1-H3(K4ME3-K9ME2) complex”. X-ray diffraction, 13 pockets (best druggability 0.53). MolNFT v1 #174400 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7BU9
Type: protein
Length: 854 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spindlin-1; H3(K4ME3-K9ME2) peptide
UniProt: Q9Y657, Q71DI3
Pockets: 13 · best druggability 0.53

Structure

x-ray diffraction · 6 distinct chains · 6% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spindlin-1	protein	204	6% helix, 39% strand	Q9Y657
B	H3(K4ME3-K9ME2) peptide	protein	9	33% helix, 11% strand	Q71DI3
C	Spindlin-1	protein	205	6% helix, 39% strand	Q9Y657
D, F, H	H3(K4ME3-K9ME2) peptide	protein	10	30% helix, 0% strand	Q71DI3
E	Spindlin-1	protein	206	4% helix, 34% strand	Q9Y657
G	Spindlin-1	protein	200	6% helix, 43% strand	Q9Y657

Pockets

13 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	346	0.53	0.73	30	empty
2	150	0.51	0.79	24	empty
3	189	0.51	0.78	33	empty
4	131	0.49	0.79	27	empty
5	92	0.42	0.78	20	empty

Interfaces

8 interfaces between chains.

A–C · 1104 Å² buried · 7 hydrogen bonds · protein-protein
E–G · 975 Å² buried · 9 hydrogen bonds · protein-protein
G–H · 866 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 821 Å² buried · 6 hydrogen bonds · protein-protein
E–F · 812 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (methylation).

Compared structures

7BU9 · Crystal Structure of Spindlin1-H3(K4me3-K9me2) complex · the same entry in another collection · chain H against H, TM-score 1.00
Q9Y657 · AlphaFold monomer V2.0 prediction for spindlin-1 (Q9Y657) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 Q9Y657
Every structure of UniProt Q71DI3
Elsewhere: RCSB PDB 7BU9 · PDBe 7BU9 · UniProt Q9Y657 · UniProt Q71DI3

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