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HIV-1 rev ntd dimers with variable crossing angles

Analyse HIV-1 rev ntd dimers with variable crossing angles in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5DHV
Type: protein
Length: 579 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Anti-rev antibody Fab single-chain variable fragment, heavy chain; Anti-rev antibody Fab…
UniProt: Q76PP8
Ligands: CL
Pockets: 3 · best druggability 0.36

Structure

x-ray diffraction · 5 distinct chains · 21% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Anti-rev antibody Fab single-chain variable fragment, heavy chain	protein	123	2% helix, 50% strand	—
B, L	Anti-rev antibody Fab single-chain variable fragment, light chain	protein	110	3% helix, 51% strand	—
H	Anti-rev antibody Fab single-chain variable fragment, heavy chain	protein	117	3% helix, 52% strand	—
M	Protein rev	protein	61	74% helix, 0% strand	Q76PP8
N	Protein rev	protein	58	78% helix, 0% strand	Q76PP8

Ligands and binding sites

CL · Chloride ion · ion · 2 copies · chains A, B, H, L

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	83	0.36	0.76	18	CL
2	66	0.32	0.76	15	CL
3	52	0.24	0.73	16	empty

Interfaces

7 interfaces between chains.

A–B · 927 Å² buried · 8 hydrogen bonds · protein-protein
H–L · 922 Å² buried · 8 hydrogen bonds · protein-protein
H–M · 432 Å² buried · 5 hydrogen bonds · protein-protein
A–N · 422 Å² buried · 5 hydrogen bonds · protein-protein
L–M · 402 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5DHV · HIV-1 Rev NTD dimers with variable crossing angles · 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 Q76PP8
Elsewhere: RCSB PDB 5DHV · PDBe 5DHV · UniProt Q76PP8

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