MolNFT v1 · #124000 · protein

Caspase-7 S239E phosphomimetic

5K20 · Caspase-7 large subunit: “Caspase-7 S239E phosphomimetic”. X-ray diffraction, 3 pockets (best druggability 0.77). MolNFT v1 #124000 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5K20
Type: protein
Length: 465 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-7 large subunit; Caspase-7 small subunit
EC: 3.4.22.60
UniProt: P55210
Pockets: 3 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 32% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Caspase-7 large subunit (EC 3.4.22.60)	protein	140	31% helix, 30% strand	P55210
B	Caspase-7 small subunit (EC 3.4.22.60)	protein	92	34% helix, 16% strand	P55210
D	Caspase-7 small subunit (EC 3.4.22.60)	protein	93	33% helix, 16% strand	P55210

Ligands and binding sites

FMT · Formic acid · additive · 3 copies · chains A, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	513	0.77	0.84	52	empty
2	123	0.41	0.75	29	empty
3	107	0.38	0.75	22	empty

Interfaces

6 interfaces between chains.

A–B · 2153 Å² buried · 29 hydrogen bonds · protein-protein
C–D · 2134 Å² buried · 30 hydrogen bonds · protein-protein
B–D · 1377 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 417 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 391 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5K20 · Caspase-7 S239E Phosphomimetic · the same entry in another collection · chain D against D, TM-score 1.00
P55210 · AlphaFold monomer V2.0 prediction for caspase-7 (P55210) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P55210
Elsewhere: RCSB PDB 5K20 · PDBe 5K20 · UniProt P55210

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