MolNFT v1 · #89510 · protein

Crystal structure of mhf complex

4DRA · Centromere protein S: “Crystal structure of mhf complex”. X-ray diffraction, 5 pockets (best druggability 0.75). MolNFT v1 #89510 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4DRA
Type: protein
Length: 677 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Centromere protein S; Centromere protein X
UniProt: Q8N2Z9, A8MT69
Pockets: 5 · best druggability 0.75

Structure

x-ray diffraction · 6 distinct chains · 76% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Centromere protein S	protein	93	78% helix, 3% strand	Q8N2Z9
B	Centromere protein S	protein	95	79% helix, 3% strand	Q8N2Z9
C	Centromere protein S	protein	98	81% helix, 3% strand	Q8N2Z9
D	Centromere protein S	protein	93	77% helix, 3% strand	Q8N2Z9
E, F, G	Centromere protein X	protein	74	69% helix, 4% strand	A8MT69
H	Centromere protein X	protein	76	67% helix, 4% strand	A8MT69

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	1012	0.75	0.78	85	empty
2	254	0.60	0.80	29	empty
3	145	0.41	0.74	28	empty
4	69	0.36	0.77	9	empty
5	52	0.28	0.74	9	empty

Interfaces

16 interfaces between chains.

D–H · 2382 Å² buried · 23 hydrogen bonds · protein-protein
B–F · 2367 Å² buried · 17 hydrogen bonds · protein-protein
C–G · 2274 Å² buried · 19 hydrogen bonds · protein-protein
A–E · 2258 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 568 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

4DRA · Crystal structure of MHF complex · the same entry in another collection · chain H against H, TM-score 1.00
A8MT69 · AlphaFold monomer V2.0 prediction for centromere protein X (A8MT69) · a predicted model of the same protein · chain E against A, TM-score 0.99
Q8N2Z9 · AlphaFold monomer V2.0 prediction for centromere protein S (Q8N2Z9) · a predicted model of the same protein · chain C 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 Q8N2Z9
Every structure of UniProt A8MT69
Elsewhere: RCSB PDB 4DRA · PDBe 4DRA · UniProt Q8N2Z9 · UniProt A8MT69

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