MolNFT v1 · #118099 · protein

Gephe in complex with MN(2+) - ADP

5ERT · Gephyrin: “Gephe in complex with MN(2+) - ADP”. X-ray diffraction, 3 ligands (ADP, MN, PO4), 6 pockets (best druggability 0.39). MolNFT v1 #118099 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5ERT
Type: protein
Length: 415 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gephyrin
EC: 2.7.7.75, 2.10.1.1
UniProt: Q03555
Ligands: ADP, MN, PO4
Pockets: 6 · best druggability 0.39

Structure

x-ray diffraction · 1 distinct chain · 20% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Gephyrin (EC 2.7.7.75, 2.10.1.1)	protein	415	20% helix, 34% strand	Q03555

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains A
MN · Manganese (II) ion · metal · 2 copies · chains A
PO4 · Phosphate ion · ion · 2 copies · chains A
ACT · Acetate ion · additive · 3 copies · chains A
MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A

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

Pockets

6 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	109	0.39	0.75	19	empty
2	66	0.35	0.77	18	empty
3	61	0.33	0.76	12	ACT
4	57	0.33	0.78	18	ADP, MN
5	58	0.28	0.74	16	empty

Compared structures

5ERT · GephE in complex with Mn(2+) - ADP · the same entry in another collection · chain A against A, TM-score 1.00
Q03555 · AlphaFold monomer V2.0 prediction for gephyrin (Q03555) · a predicted model of the same protein · chain A 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 Q03555
Elsewhere: RCSB PDB 5ERT · PDBe 5ERT · UniProt Q03555

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