MolNFT v1 · #108390 · protein

New structural conformations of adenylate kinase from streptococcus pneumoniae D39

4W5H: “New structural conformations of adenylate kinase from streptococcus pneumoniae D39”. X-ray diffraction, 1 pocket (best druggability 0.61). MolNFT v1 #108390 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4W5H
Type: protein
Length: 208 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adenylate kinase
EC: 2.7.4.3
UniProt: Q04ML5
Pockets: 1 · best druggability 0.61

Structure

x-ray diffraction · 1 distinct chain · 55% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Adenylate kinase (EC 2.7.4.3)	protein	208	55% helix, 16% strand	Q04ML5

Ligands and binding sites

TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	170	0.61	0.83	28	empty

Compared structures

4W5H · New structural conformations of adenylate kinase from Streptococcus pneumoniae D39 · the same entry in another collection · chain A against A, TM-score 1.00
Q04ML5 · AlphaFold monomer V2.0 prediction for adenylate kinase (Q04ML5) · a predicted model of the same protein · chain A against A, TM-score 0.72

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 Q04ML5
Elsewhere: RCSB PDB 4W5H · PDBe 4W5H · UniProt Q04ML5

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