MolNFT v1 · #106862 · protein

Crystal structure of helicobacter pylori HP1029

4TSD: “Crystal structure of helicobacter pylori HP1029”. X-ray diffraction, 1 ligand (ZN), 6 pockets (best druggability 0.64). MolNFT v1 #106862 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4TSD
Type: protein
Length: 360 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HP1029
UniProt: O25673
Ligands: ZN
Pockets: 6 · best druggability 0.64

Structure

x-ray diffraction · 2 distinct chains · 21% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	HP1029	protein	181	23% helix, 45% strand	O25673
A	HP1029	protein	179	20% helix, 44% strand	O25673

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains B, A
EDO · 1,2-ethanediol · additive · chains B, 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	133	0.64	0.87	34	empty
2	160	0.61	0.84	33	EDO
3	193	0.50	0.77	26	empty
4	175	0.49	0.77	24	empty
5	72	0.48	0.83	18	empty

Interfaces

1 interface between chains.

B–A · 1740 Å² buried · 27 hydrogen bonds · protein-protein

Compared structures

4TSD · Crystal structure of Helicobacter pylori HP1029 · the same entry in another collection · chain B against B, 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 O25673
Elsewhere: RCSB PDB 4TSD · PDBe 4TSD · UniProt O25673

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