MolNFT v1 · #137223 · protein

GLUA2-2XGSG1L bound to zk

5VHY · Glutamate receptor 2,GERM cell-specific gene 1-like protein: “GLUA2-2XGSG1L bound to zk”. Electron microscopy, 2 ligands (ZK1, NAG), 20 pockets (best druggability 0.85). MolNFT v1 #137223 on GenesisL1: 3D structure, binding sites…

PDB: 5VHY
Type: protein
Length: 3,484 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutamate receptor 2,GERM cell-specific gene 1-like protein
UniProt: P19491, D3ZK93
Ligands: ZK1, NAG
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 3 distinct chains · 45% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Glutamate receptor 2,GERM cell-specific gene 1-like protein	protein	783	44% helix, 16% strand	P19491, D3ZK93
B, D	Glutamate receptor 2,GERM cell-specific gene 1-like protein	protein	780	42% helix, 15% strand	P19491, D3ZK93
E, F	Glutamate receptor 2,GERM cell-specific gene 1-like protein	protein	179	64% helix, 6% strand	P19491, D3ZK93

Ligands and binding sites

ZK1 · {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid · ligand · 4 copies · chains A, B, C, D
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1006	0.85	0.86	116	empty
2	357	0.85	0.94	28	empty
3	612	0.84	0.89	88	empty
4	672	0.77	0.83	63	empty
5	253	0.77	0.90	39	empty

Interfaces

10 interfaces between chains.

C–D · 3537 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 3519 Å² buried · 20 hydrogen bonds · protein-protein
B–C · 3352 Å² buried · 19 hydrogen bonds · protein-protein
A–D · 3293 Å² buried · 20 hydrogen bonds · protein-protein
C–F · 679 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

5VHY · GluA2-2xGSG1L bound to ZK · the same entry in another collection · chain F against F, TM-score 1.00
D3ZK93 · AlphaFold monomer V2.0 prediction for germ cell-specific gene 1-like protein (D3ZK93) · a predicted model of the same protein · chain E against A, TM-score 0.91

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 P19491
Every structure of UniProt D3ZK93
Elsewhere: RCSB PDB 5VHY · PDBe 5VHY · UniProt P19491 · UniProt D3ZK93

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