MolNFT v1 · #134184 · protein

Crystal structure of P53 epitope-scaffold based on a inhibitor of cysteine proteases in complex with human MDM2

5SWK · E3 ubiquitin-protein ligase MDM2: “Crystal structure of P53 epitope-scaffold based on a inhibitor of cysteine proteases in complex with human…”. X-ray diffraction, 2 ligands (CL, SO4), 1 pocket (best druggability 0.77). MolNFT v1…

PDB: 5SWK
Type: protein
Length: 370 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 ubiquitin-protein ligase MDM2; De novo protein based on the inhibitor amoebiasin-1
EC: 6.3.2.-
UniProt: Q00987
Ligands: CL, SO4
Pockets: 1 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 27% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-)	protein	84	44% helix, 17% strand	Q00987
B	E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-)	protein	85	45% helix, 19% strand	Q00987
C	De novo protein based on the inhibitor amoebiasin-1	protein	100	12% helix, 59% strand	—
D	De novo protein based on the inhibitor amoebiasin-1	protein	101	12% helix, 59% strand	—

Ligands and binding sites

CL · Chloride ion · ion · 7 copies · chains A, B, D
SO4 · Sulfate ion · ion · 2 copies · chains B, C, D
GOL · Glycerol · additive · chains C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	723	0.77	0.81	57	CL

Interfaces

5 interfaces between chains.

C–D · 2071 Å² buried · 46 hydrogen bonds · protein-protein
A–C · 672 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 647 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 364 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 30 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5SWK · Crystal structure of p53 epitope-scaffold based on a inhibitor of cysteine proteases in… · 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 Q00987
Elsewhere: RCSB PDB 5SWK · PDBe 5SWK · UniProt Q00987

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