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Crystal structure of human nucleophosmin-core in complex with cytochrome C

Analyse Crystal structure of human nucleophosmin-core in complex with cytochrome C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5EHD
Type: protein
Length: 2,125 residues
Chains: 20
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleophosmin
UniProt: P06748
Ligands: CL
Pockets: 15 · best druggability 0.89

Structure

x-ray diffraction · 5 distinct chains · 0% helix, 65% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, G, a, c, f, g	Nucleophosmin	protein	106	0% helix, 64% strand	P06748
B, D, b	Nucleophosmin	protein	105	0% helix, 65% strand	P06748
C, F, H, I, d, e, i	Nucleophosmin	protein	107	0% helix, 64% strand	P06748
J	Nucleophosmin	protein	107	0% helix, 65% strand	P06748
h, j	Nucleophosmin	protein	106	0% helix, 64% strand	P06748

Ligands and binding sites

CL · Chloride ion · ion · 4 copies · chains A, B, C, D, E, F, G, H, I, J, a, b, c, d, e, f, g, i, j

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

Pockets

15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	871	0.89	0.91	93	CL
2	615	0.86	0.91	64	CL
3	307	0.82	0.92	39	empty
4	421	0.63	0.77	56	empty
5	79	0.53	0.85	21	empty

Interfaces

35 interfaces between chains.

F–J · 1103 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1092 Å² buried · 20 hydrogen bonds · protein-protein
B–C · 1078 Å² buried · 18 hydrogen bonds · protein-protein
g–h · 1070 Å² buried · 15 hydrogen bonds · protein-protein
f–j · 1066 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

5EHD · Crystal structure of human nucleophosmin-core in complex with cytochrome c · 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 P06748
Elsewhere: RCSB PDB 5EHD · PDBe 5EHD · UniProt P06748

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