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Structure of cisptnap-NCP145

Analyse Structure of cisptnap-NCP145 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4WU9
Type: protein + DNA
Length: 1,053 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.2; Histone H4; Histone H2A type 1; Histone H2B 1.1; DNA (145-mer)
UniProt: P84233, P62799, P06897, P02281
Ligands: CX8, MG, SO4
Pockets: 20 · best druggability 0.74

Structure

x-ray diffraction · 7 distinct chains · 63% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Histone H3.2	protein	96	67% helix, 4% strand	P84233
B	Histone H4	protein	82	60% helix, 7% strand	P62799
C, G	Histone H2A type 1	protein	106	56% helix, 7% strand	P06897
D, H	Histone H2B 1.1	protein	95	74% helix, 4% strand	P02281
F	Histone H4	protein	87	57% helix, 8% strand	P62799
I	DNA (145-mer)	dna	145	—	—
J	DNA (145-mer)	dna	145	—	—

Ligands and binding sites

CX8 · [2-{3-[(2-{[2-(amino-kappan)ethyl]amino-kappan}ethyl) amino-kappan]propyl}-1H-benzo[de]isoquinoline-1,3(2H)-dionato(3-)]platinum · ligand · 3 copies · chains I, J
MG · Magnesium ion · metal · chains E, F
SO4 · Sulfate ion · ion · 2 copies · chains C, D, J, G, H, I

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	331	0.74	0.86	45	empty
2	499	0.73	0.82	63	empty
3	301	0.73	0.86	44	empty
4	320	0.69	0.83	47	empty
5	684	0.67	0.76	46	empty

Interfaces

38 interfaces between chains.

I–J · 6397 Å² buried · 583 hydrogen bonds · nucleic-nucleic
E–F · 2664 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 2622 Å² buried · 26 hydrogen bonds · protein-protein
G–H · 2616 Å² buried · 28 hydrogen bonds · protein-protein
A–B · 2547 Å² buried · 28 hydrogen bonds · protein-protein

Compared structures

4WU9 · Structure of cisPtNAP-NCP145 · the same entry in another collection · chain J against J, TM-score 1.00
P06897 · AlphaFold monomer V2.0 prediction for histone H2A type 1 (P06897) · a predicted model of the same protein · chain C 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 P84233
Every structure of UniProt P62799
Every structure of UniProt P06897
Every structure of UniProt P02281
Elsewhere: RCSB PDB 4WU9 · PDBe 4WU9 · UniProt P84233 · UniProt P62799 · UniProt P06897 · UniProt P02281

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