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Crystal structure of CA2+-bound form of DES3-23ALG-2

Analyse Crystal structure of CA2+-bound form of DES3-23ALG-2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2ZRS
Type: protein
Length: 1,309 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Programmed cell death protein 6
UniProt: O75340
Ligands: CA
Pockets: 15 · best druggability 0.82

Structure

x-ray diffraction · 5 distinct chains · 49% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Programmed cell death protein 6	protein	165	39% helix, 1% strand	O75340
B, F, G, H	Programmed cell death protein 6	protein	163	53% helix, 4% strand	O75340
C	Programmed cell death protein 6	protein	162	48% helix, 4% strand	O75340
D	Programmed cell death protein 6	protein	164	50% helix, 6% strand	O75340
E	Programmed cell death protein 6	protein	166	55% helix, 4% strand	O75340

Ligands and binding sites

CA · Calcium ion · metal · 25 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

15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	752	0.82	0.85	63	empty
2	961	0.81	0.83	67	empty
3	868	0.80	0.82	59	empty
4	724	0.77	0.81	60	CA
5	329	0.70	0.83	43	empty

Interfaces

8 interfaces between chains.

E–F · 1492 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 1430 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 1210 Å² buried · 16 hydrogen bonds · protein-protein
G–H · 1022 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 883 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

2ZRS · Crystal structure of Ca2+-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 D 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 2ZRS · PDBe 2ZRS · UniProt O75340

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