MolNFT v1 · #107690 · protein

Crystal structure of the pyocin AP41 DNase

4UHQ · Large component of pyocin AP41: “Crystal structure of the pyocin AP41 DNase”. X-ray diffraction, 1 ligand (NI), 3 pockets (best druggability 0.47). MolNFT v1 #107690 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4UHQ
Type: protein
Length: 267 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Large component of pyocin AP41
UniProt: Q51502
Ligands: NI
Pockets: 3 · best druggability 0.47

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Large component of pyocin AP41	protein	133	44% helix, 17% strand	Q51502
B	Large component of pyocin AP41	protein	134	43% helix, 16% strand	Q51502

Ligands and binding sites

NI · Nickel (II) ion · metal · 2 copies · chains A, B
CIT · Citric acid · additive · 3 copies · chains A, B

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

Pockets

3 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	204	0.47	0.74	29	CIT
2	164	0.42	0.74	30	CIT
3	136	0.41	0.74	23	empty

Interfaces

1 interface between chains.

A–B · 277 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

4UHQ · Crystal structure of the pyocin AP41 DNase · the same entry in another collection · chain A against A, TM-score 1.00

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 Q51502
Elsewhere: RCSB PDB 4UHQ · PDBe 4UHQ · UniProt Q51502

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