MolNFT v1 · #56827 · protein

Crystal structure of ZN2+-bound form of DES3-23ALG-2

2ZRT · Programmed cell death protein 6: “Crystal structure of ZN2+-bound form of DES3-23ALG-2”. X-ray diffraction, 1 ligand (ZN), 19 pockets (best druggability 0.82). MolNFT v1 #56827 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 2ZRT
Type: protein
Length: 1,314 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Programmed cell death protein 6
UniProt: O75340
Ligands: ZN
Pockets: 19 · best druggability 0.82

Structure

x-ray diffraction · 6 distinct chains · 50% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F	Programmed cell death protein 6	protein	165	38% helix, 2% strand	O75340
B	Programmed cell death protein 6	protein	165	54% helix, 4% strand	O75340
C	Programmed cell death protein 6	protein	164	58% helix, 8% strand	O75340
D	Programmed cell death protein 6	protein	163	58% helix, 6% strand	O75340
E	Programmed cell death protein 6	protein	166	54% helix, 4% strand	O75340
G, H	Programmed cell death protein 6	protein	163	37% helix, 3% strand	O75340

Ligands and binding sites

ZN · Zinc ion · metal · 37 copies · chains A, B, C, D, E, F, G, H

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

Pockets

19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	737	0.82	0.86	59	empty
2	918	0.82	0.84	77	empty
3	723	0.82	0.85	49	empty
4	171	0.75	0.91	26	empty
5	976	0.74	0.77	57	empty

Interfaces

8 interfaces between chains.

A–B · 1665 Å² buried · 23 hydrogen bonds · protein-protein
E–F · 1462 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 1405 Å² buried · 16 hydrogen bonds · protein-protein
G–H · 1297 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 893 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

2ZRT · Crystal structure of Zn2+-bound form of des3-23ALG-2 · the same entry in another collection · chain E against E, 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 C against A, TM-score 0.98

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 2ZRT · PDBe 2ZRT · UniProt O75340

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