MolNFT v1 · #88656 · protein

Tetramerization domain of zebrafish P53 (crystal form II)

4D1M · Cellular tumor antigen P53: “Tetramerization domain of zebrafish P53 (crystal form II)”. X-ray diffraction, 1 ligand (ZN), 9 pockets (best druggability 0.67). MolNFT v1 #88656 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4D1M
Type: protein
Length: 476 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cellular tumor antigen P53
UniProt: G1K2L5
Ligands: ZN
Pockets: 9 · best druggability 0.67

Structure

x-ray diffraction · 7 distinct chains · 68% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cellular tumor antigen P53	protein	38	68% helix, 18% strand	G1K2L5
B, H	Cellular tumor antigen P53	protein	40	70% helix, 18% strand	G1K2L5
C, K	Cellular tumor antigen P53	protein	40	68% helix, 18% strand	G1K2L5
D, I, J, L	Cellular tumor antigen P53	protein	39	69% helix, 18% strand	G1K2L5
E	Cellular tumor antigen P53	protein	42	69% helix, 17% strand	G1K2L5
F	Cellular tumor antigen P53	protein	41	66% helix, 17% strand	G1K2L5
G	Cellular tumor antigen P53	protein	39	67% helix, 18% strand	G1K2L5

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B, F

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

Pockets

9 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	544	0.67	0.77	38	empty
2	567	0.66	0.77	51	empty
3	130	0.40	0.75	20	empty
4	58	0.39	0.79	11	empty
5	67	0.36	0.77	12	empty

Interfaces

34 interfaces between chains.

C–D · 1227 Å² buried · 17 hydrogen bonds · protein-protein
G–H · 1224 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1213 Å² buried · 16 hydrogen bonds · protein-protein
K–L · 1211 Å² buried · 16 hydrogen bonds · protein-protein
I–J · 1195 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

4D1M · Tetramerization domain of zebrafish p53 (crystal form II) · 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 G1K2L5
Elsewhere: RCSB PDB 4D1M · PDBe 4D1M · UniProt G1K2L5

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