MolNFT v1 · #185004 · protein

Crystal structure of the cenp-opqur complex

7PB8 · Centromere protein O: “Crystal structure of the cenp-opqur complex”. X-ray diffraction, 15 pockets (best druggability 0.76). MolNFT v1 #185004 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7PB8
Type: protein
Length: 706 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Centromere protein O; Centromere protein Q; Centromere protein U; Centromere protein P…
UniProt: Q9BU64, Q7L2Z9, Q71F23, Q6IPU0, Q13352
Pockets: 15 · best druggability 0.76

Structure

x-ray diffraction · 5 distinct chains · 51% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
O	Centromere protein O	protein	198	37% helix, 25% strand	Q9BU64
Q	Centromere protein Q	protein	112	75% helix, 0% strand	Q7L2Z9
U	Centromere protein U	protein	103	76% helix, 1% strand	Q71F23
P	Centromere protein P	protein	224	38% helix, 29% strand	Q6IPU0
R	Centromere protein R	protein	69	59% helix, 0% strand	Q13352

Pockets

15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	554	0.76	0.83	44	empty
2	116	0.76	0.95	28	empty
3	163	0.67	0.87	31	empty
4	178	0.63	0.83	28	empty
5	67	0.62	0.91	15	empty

Interfaces

7 interfaces between chains.

Q–U · 2075 Å² buried · 7 hydrogen bonds · protein-protein
U–P · 1955 Å² buried · 15 hydrogen bonds · protein-protein
O–P · 1904 Å² buried · 8 hydrogen bonds · protein-protein
Q–P · 1350 Å² buried · 8 hydrogen bonds · protein-protein
U–R · 847 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

7PB8 · Crystal structure of the CENP-OPQUR complex · the same entry in another collection · chain R against R, TM-score 1.00
Q6IPU0 · AlphaFold monomer V2.0 prediction for centromere protein P (Q6IPU0) · a predicted model of the same protein · chain P against A, TM-score 0.90
Q9BU64 · AlphaFold monomer V2.0 prediction for centromere protein O (Q9BU64) · a predicted model of the same protein · chain O against A, TM-score 0.87
Q71F23 · AlphaFold monomer V2.0 prediction for centromere protein U (Q71F23) · a predicted model of the same protein · chain U against A, TM-score 0.53
Q13352 · AlphaFold monomer V2.0 prediction for centromere protein R (Q13352) · a predicted model of the same protein · chain R against A, TM-score 0.46
Q7L2Z9 · AlphaFold monomer V2.0 prediction for centromere protein Q (Q7L2Z9) · a predicted model of the same protein · chain Q against A, TM-score 0.37

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 Q9BU64
Every structure of UniProt Q7L2Z9
Every structure of UniProt Q71F23
Every structure of UniProt Q6IPU0
Every structure of UniProt Q13352
Elsewhere: RCSB PDB 7PB8 · PDBe 7PB8 · UniProt Q9BU64 · UniProt Q7L2Z9 · UniProt Q71F23 · UniProt Q6IPU0 · UniProt Q13352

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