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Structure of HIV cleaved synaptic complex (csc) intasome bound with magnesium and insti XZ446 (compound 4F)

Analyse Structure of HIV cleaved synaptic complex (csc) intasome bound with magnesium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6PUZ
Type: protein + DNA
Length: 651 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chimeric SSO7D and HIV-1 integrase; Viral DNA non-transferred strand; Viral DNA…
UniProt: P39476, Q76353
Ligands: XXJ, MG, ZN
Pockets: 11 · best druggability 0.67

Structure

electron microscopy · 6 distinct chains · 38% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Chimeric SSO7D and HIV-1 integrase	protein	262	43% helix, 18% strand	P39476, Q76353
B	Chimeric SSO7D and HIV-1 integrase	protein	240	44% helix, 25% strand	P39476, Q76353
C	Chimeric SSO7D and HIV-1 integrase	protein	65	15% helix, 45% strand	P39476, Q76353
D	Chimeric SSO7D and HIV-1 integrase	protein	48	6% helix, 60% strand	P39476, Q76353
E	Viral DNA non-transferred strand	dna	19	—	—
F	Viral DNA transferred strand	dna	17	—	—

Ligands and binding sites

XXJ · 4-azanyl-N-[[2,4-bis(fluoranyl)phenyl]methyl]-1-oxidanyl-2-oxidanylidene-6-[2-(phenylsulfonyl)ethyl]-1,8-naphthyridine-3-carboxamide · ligand · chains A, E, F
MG · Magnesium ion · metal · 2 copies · chains A, F
ZN · Zinc ion · metal · 2 copies · chains A, B

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

Pockets

11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	603	0.67	0.77	58	empty
2	420	0.63	0.77	45	empty
3	283	0.55	0.76	28	empty
4	295	0.53	0.75	32	empty
5	120	0.47	0.78	18	empty

Interfaces

12 interfaces between chains.

A–C · 1641 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1638 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 831 Å² buried · 13 hydrogen bonds · protein-protein
A–E · 732 Å² buried · 18 hydrogen bonds · protein-nucleic
E–F · 710 Å² buried · 50 hydrogen bonds · nucleic-nucleic

Compared structures

6PUZ · Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI… · the same entry in another collection · chain F against F, TM-score 1.00
P39476 · AlphaFold monomer V2.0 prediction for DNA-binding protein 7D (P39476) · a predicted model of the same protein · chain D against A, TM-score 0.50

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 P39476
Every structure of UniProt Q76353
Elsewhere: RCSB PDB 6PUZ · PDBe 6PUZ · UniProt P39476 · UniProt Q76353

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