MolNFT v1 · #821 · protein

Catalytic domain of bacteriophage HP1 integrase

1AIH: “Catalytic domain of bacteriophage HP1 integrase”. X-ray diffraction, 2 ligands (MG, SO4), 3 pockets (best druggability 0.43). MolNFT v1 #821 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1AIH
Type: protein
Length: 676 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HP1 integrase
UniProt: P21442
Ligands: MG, SO4
Pockets: 3 · best druggability 0.43

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	HP1 integrase	protein	170	46% helix, 8% strand	P21442
B, C	HP1 integrase	protein	168	49% helix, 8% strand	P21442

Ligands and binding sites

MG · Magnesium ion · metal · 5 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D

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	117	0.43	0.77	25	empty
2	104	0.39	0.76	24	empty
3	96	0.34	0.73	19	empty

Interfaces

3 interfaces between chains.

C–D · 2113 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 2097 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 459 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

1AIH · Catalytic domain of bacteriophage HP1 integrase · 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 P21442
Elsewhere: RCSB PDB 1AIH · PDBe 1AIH · UniProt P21442

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