MolNFT v1 · #116795 · protein

P2 integrase catalytic domain in space group P21

5DOR: “P2 integrase catalytic domain in space group P21”. X-ray diffraction, 2 ligands (ZN, PO4), 4 pockets (best druggability 0.69). MolNFT v1 #116795 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5DOR
Type: protein
Length: 638 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Integrase
UniProt: P36932
Ligands: ZN, PO4
Pockets: 4 · best druggability 0.69

Structure

x-ray diffraction · 4 distinct chains · 54% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Integrase	protein	162	53% helix, 7% strand	P36932
B	Integrase	protein	161	53% helix, 7% strand	P36932
C	Integrase	protein	158	54% helix, 8% strand	P36932
D	Integrase	protein	157	55% helix, 8% strand	P36932

Ligands and binding sites

ZN · Zinc ion · metal · chains B
PO4 · Phosphate ion · ion · chains B

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

Pockets

4 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	227	0.69	0.85	40	empty
2	358	0.58	0.76	36	empty
3	133	0.51	0.80	27	empty
4	96	0.35	0.74	17	empty

Interfaces

4 interfaces between chains.

A–B · 2082 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 2080 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 399 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 331 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5DOR · P2 Integrase catalytic domain in space group P21 · 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 P36932
Elsewhere: RCSB PDB 5DOR · PDBe 5DOR · UniProt P36932

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