MolNFT v1 · #29991 · protein

Act domain protein from streptococcus pneumoniae

1ZPV: “Act domain protein from streptococcus pneumoniae”. X-ray diffraction, 1 ligand (K), 2 pockets (best druggability 0.44). MolNFT v1 #29991 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1ZPV
Type: protein
Length: 257 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Act domain protein
UniProt: P67382
Ligands: K
Pockets: 2 · best druggability 0.44

Structure

x-ray diffraction · 3 distinct chains · 34% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Act domain protein	protein	85	34% helix, 42% strand	P67382
B	Act domain protein	protein	84	36% helix, 43% strand	P67382
C	Act domain protein	protein	88	33% helix, 41% strand	P67382

Ligands and binding sites

K · Potassium ion · metal · chains A, C

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

Pockets

2 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	72	0.44	0.81	17	empty
2	52	0.34	0.79	17	empty

Interfaces

3 interfaces between chains.

A–C · 1177 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 416 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 13 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 modified (engineered).

Compared structures

1ZPV · ACT domain protein from Streptococcus pneumoniae · the same entry in another collection · chain A against A, TM-score 1.00
P67382 · AlphaFold monomer V2.0 prediction for UPF0237 protein SP_0238 (P67382) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 P67382
Elsewhere: RCSB PDB 1ZPV · PDBe 1ZPV · UniProt P67382

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