MolNFT v1 · #115956 · protein

Crystal structure of the catalytic core domain of mmtv integrase

5CZ1: “Crystal structure of the catalytic core domain of mmtv integrase”. X-ray diffraction, 13 pockets (best druggability 0.76). MolNFT v1 #115956 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5CZ1
Type: protein
Length: 616 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Integrase
UniProt: O56220
Pockets: 13 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 48% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Integrase	protein	162	46% helix, 19% strand	O56220
B	Integrase	protein	150	50% helix, 18% strand	O56220
C	Integrase	protein	161	48% helix, 17% strand	O56220
D	Integrase	protein	143	49% helix, 19% strand	O56220

Pockets

13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	630	0.76	0.82	76	empty
2	594	0.76	0.82	70	empty
3	94	0.46	0.80	16	empty
4	85	0.43	0.79	15	empty
5	86	0.42	0.79	19	empty

Interfaces

6 interfaces between chains.

C–D · 908 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 908 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 743 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 731 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 430 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5CZ1 · Crystal structure of the catalytic core domain of MMTV 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 O56220
Elsewhere: RCSB PDB 5CZ1 · PDBe 5CZ1 · UniProt O56220

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