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Crystal structure of P73 DNA binding domain complex bound with 1 bp and 2 bp spacer DNA response elements.

Analyse Crystal structure of P73 DNA binding domain complex bound with 1 bp and 2 bp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7EZJ
Type: protein + DNA
Length: 3,387 residues
Chains: 32
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tumor protein P73; 12-mer DNA
UniProt: O15350
Ligands: ZN
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 13 distinct chains · 10% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tumor protein P73	protein	202	9% helix, 34% strand	O15350
B, C, K, i	Tumor protein P73	protein	201	11% helix, 32% strand	O15350
D, I, a	Tumor protein P73	protein	199	12% helix, 34% strand	O15350
J	Tumor protein P73	protein	197	10% helix, 31% strand	O15350
L, l	Tumor protein P73	protein	200	11% helix, 33% strand	O15350
b	Tumor protein P73	protein	199	8% helix, 33% strand	O15350
c	Tumor protein P73	protein	200	10% helix, 33% strand	O15350
d	Tumor protein P73	protein	198	8% helix, 33% strand	O15350
j	Tumor protein P73	protein	196	10% helix, 32% strand	O15350
k	Tumor protein P73	protein	206	9% helix, 33% strand	O15350
E, e	12-mer DNA	dna	11	—	—
F, f	12-mer DNA	dna	11	—	—
G, H, M, N, O, P, g, h, m, n, o, p	12-mer DNA	dna	12	—	—

Ligands and binding sites

ZN · Zinc ion · metal · 16 copies · chains A, B, C, D, I, J, K, L, a, b, c, d, i, j, k, l

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	940	0.81	0.83	106	empty
2	759	0.78	0.82	78	empty
3	1101	0.78	0.80	99	empty
4	1004	0.78	0.80	99	empty
5	684	0.78	0.83	60	empty

Interfaces

82 interfaces between chains.

B–I · 762 Å² buried · 4 hydrogen bonds · protein-protein
b–i · 751 Å² buried · 6 hydrogen bonds · protein-protein
b–c · 690 Å² buried · 7 hydrogen bonds · protein-protein
a–d · 636 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 628 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

7EZJ · Crystal structure of p73 DNA binding domain complex bound with 1 bp and 2 bp spacer DNA… · the same entry in another collection · chain j against j, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt O15350
Elsewhere: RCSB PDB 7EZJ · PDBe 7EZJ · UniProt O15350

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