MolNFT v1 · #102927 · protein

Crystal structure of human centromere protein M

4P0T: “Crystal structure of human centromere protein M”. X-ray diffraction, 4 pockets (best druggability 0.58). MolNFT v1 #102927 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4P0T
Type: protein
Length: 298 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Centromere protein M
UniProt: Q9NSP4
Pockets: 4 · best druggability 0.58

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Centromere protein M	protein	148	42% helix, 19% strand	Q9NSP4
B	Centromere protein M	protein	150	43% helix, 19% strand	Q9NSP4

Ligands and binding sites

GOL · Glycerol · additive · chains B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

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	214	0.58	0.80	32	empty
2	108	0.36	0.74	19	empty
3	66	0.35	0.78	16	empty
4	52	0.28	0.74	13	empty

Interfaces

1 interface between chains.

A–B · 718 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

4P0T · Crystal structure of human centromere protein M · the same entry in another collection · chain A against A, TM-score 1.00
Q9NSP4 · AlphaFold monomer V2.0 prediction for centromere protein M (Q9NSP4) · a predicted model of the same protein · chain A 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 Q9NSP4
Elsewhere: RCSB PDB 4P0T · PDBe 4P0T · UniProt Q9NSP4

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