MolNFT v1 · #94949 · protein

Human P53 core domain with hot spot mutation R273H (form I)

4IBS · Cellular tumor antigen P53: “Human P53 core domain with hot spot mutation R273H (form I)”. X-ray diffraction, 1 ligand (ZN), 10 pockets (best druggability 0.64). MolNFT v1 #94949 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 4IBS
Type: protein
Length: 775 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cellular tumor antigen P53
UniProt: P04637
Ligands: ZN
Pockets: 10 · best druggability 0.64

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cellular tumor antigen P53	protein	193	9% helix, 34% strand	P04637
B, C, D	Cellular tumor antigen P53	protein	194	9% helix, 34% strand	P04637

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
EDO · 1,2-ethanediol · additive · chains D

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

Pockets

10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	571	0.64	0.76	78	empty
2	464	0.64	0.77	68	empty
3	307	0.53	0.75	37	empty
4	179	0.47	0.76	37	empty
5	122	0.40	0.75	19	empty

Interfaces

4 interfaces between chains.

B–C · 549 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 510 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 480 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 259 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

4IBS · Human p53 core domain with hot spot mutation R273H (form I) · 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 P04637
Elsewhere: RCSB PDB 4IBS · PDBe 4IBS · UniProt P04637

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