MolNFT v1 · #62538 · protein

Crystal structure of PDCD4

3EIJ · Programmed cell death protein 4: “Crystal structure of PDCD4”. X-ray diffraction, 5 pockets (best druggability 0.77). MolNFT v1 #62538 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3EIJ
Type: protein
Length: 552 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Programmed cell death protein 4
UniProt: Q53EL6
Pockets: 5 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 76% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Programmed cell death protein 4	protein	276	76% helix, 1% strand	Q53EL6

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	634	0.77	0.83	39	empty
2	675	0.77	0.82	42	empty
3	178	0.51	0.78	25	empty
4	161	0.50	0.78	22	empty
5	57	0.27	0.74	17	empty

Interfaces

1 interface between chains.

A–B · 1520 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

3EIJ · Crystal structure of Pdcd4 · the same entry in another collection · chain A against A, TM-score 1.00
Q53EL6 · AlphaFold monomer V2.0 prediction for programmed cell death protein 4 (Q53EL6) · a predicted model of the same protein · chain A against A, TM-score 0.55

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 Q53EL6
Elsewhere: RCSB PDB 3EIJ · PDBe 3EIJ · UniProt Q53EL6

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