MolNFT v1 · #161363 · protein

Structure of the HTLV-2 integrase catalytic core domain in complex with magnesium (dimeric form)

6QBV: “Structure of the HTLV-2 integrase catalytic core domain in complex with magnesium (dimeric form)”. X-ray diffraction, 1 ligand (MG), 11 pockets (best druggability 0.57). MolNFT v1 #161363 on GenesisL1: 3D structure, binding sites…

PDB: 6QBV
Type: protein
Length: 583 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Integrase
UniProt: Q82441
Ligands: MG
Pockets: 11 · best druggability 0.57

Structure

x-ray diffraction · 4 distinct chains · 46% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Integrase	protein	146	45% helix, 24% strand	Q82441
B	Integrase	protein	145	47% helix, 24% strand	Q82441
C	Integrase	protein	147	46% helix, 23% strand	Q82441
D	Integrase	protein	145	46% helix, 25% strand	Q82441

Ligands and binding sites

MG · Magnesium ion · metal · 4 copies · chains A, B, C, D

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

Pockets

11 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	206	0.57	0.80	27	empty
2	189	0.56	0.80	21	empty
3	216	0.47	0.74	32	empty
4	118	0.38	0.74	16	empty
5	108	0.35	0.73	17	empty

Interfaces

3 interfaces between chains.

C–D · 943 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 917 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 327 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6QBV · Structure of the HTLV-2 integrase catalytic core domain in complex with magnesium… · 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 Q82441
Elsewhere: RCSB PDB 6QBV · PDBe 6QBV · UniProt Q82441

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