MolNFT v1 · #52203 · protein

Activation of nucleoplasmin, an oligomeric histone chaperone, challenges its stability

2VTX · Npm-a protein: “Activation of nucleoplasmin, an oligomeric histone chaperone, challenges its stability”. X-ray diffraction, 3 pockets (best druggability 0.85). MolNFT v1 #52203 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 2VTX
Type: protein
Length: 928 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Npm-a protein
UniProt: Q6GQG6
Pockets: 3 · best druggability 0.85

Structure

x-ray diffraction · 10 distinct chains · 0% helix, 59% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Npm-a protein	protein	92	0% helix, 57% strand	Q6GQG6
B	Npm-a protein	protein	96	0% helix, 58% strand	Q6GQG6
C	Npm-a protein	protein	89	0% helix, 61% strand	Q6GQG6
D	Npm-a protein	protein	89	0% helix, 58% strand	Q6GQG6
E	Npm-a protein	protein	91	0% helix, 60% strand	Q6GQG6
G	Npm-a protein	protein	94	0% helix, 60% strand	Q6GQG6
H	Npm-a protein	protein	95	0% helix, 58% strand	Q6GQG6
I	Npm-a protein	protein	96	0% helix, 60% strand	Q6GQG6
J	Npm-a protein	protein	93	0% helix, 62% strand	Q6GQG6
K	Npm-a protein	protein	93	0% helix, 57% strand	Q6GQG6

Pockets

3 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	365	0.85	0.93	36	empty
2	366	0.84	0.93	35	empty
3	52	0.34	0.78	11	empty

Interfaces

10 interfaces between chains.

H–I · 936 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 933 Å² buried · 8 hydrogen bonds · protein-protein
G–H · 920 Å² buried · 9 hydrogen bonds · protein-protein
A–E · 914 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 909 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

2VTX · Activation of nucleoplasmin, an oligomeric histone chaperone, challenges its stability · the same entry in another collection · chain A against A, TM-score 1.00

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 Q6GQG6
Elsewhere: RCSB PDB 2VTX · PDBe 2VTX · UniProt Q6GQG6

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