MolNFT v1 · #56680 · protein

Crystal structure of CA2+-bound form of DES3-20ALG-2

2ZN9 · Programmed cell death protein 6: “Crystal structure of CA2+-bound form of DES3-20ALG-2”. X-ray diffraction, 1 ligand (CA), 3 pockets (best druggability 0.46). MolNFT v1 #56680 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 2ZN9
Type: protein
Length: 339 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Programmed cell death protein 6
UniProt: O75340
Ligands: CA
Pockets: 3 · best druggability 0.46

Structure

x-ray diffraction · 2 distinct chains · 57% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Programmed cell death protein 6	protein	169	57% helix, 7% strand	O75340
B	Programmed cell death protein 6	protein	170	58% helix, 5% strand	O75340

Ligands and binding sites

CA · Calcium ion · metal · 7 copies · chains A, B
2PE · Nonaethylene glycol · additive · chains A, B
12P · Dodecaethylene glycol · additive · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	171	0.46	0.75	26	empty
2	62	0.37	0.78	14	empty
3	71	0.36	0.76	16	empty

Interfaces

1 interface between chains.

A–B · 1480 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

2ZN9 · Crystal structure of Ca2+-bound form of des3-20ALG-2 · the same entry in another collection · chain A against A, TM-score 1.00
O75340 · AlphaFold monomer V2.0 prediction for programmed cell death protein 6 (O75340) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 O75340
Elsewhere: RCSB PDB 2ZN9 · PDBe 2ZN9 · UniProt O75340

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