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Structure of HIV-1 reverse transcriptase (rt) in complex with DNA and (-)ftc-tp

Analyse Structure of HIV-1 reverse transcriptase (rt) in complex with DNA and (-)ftc-tp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6OR7
Type: protein + DNA
Length: 974 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Reverse TRANSCRIPTASE/RIBONUCLEASE H; P51 rt; DNA primer 20-mer; DNA template 27-mer
EC: 2.7.7.49, 2.7.7.7, 3.1.26.13
UniProt: P04585
Ligands: 1RY, MG, SO4
Pockets: 12 · best druggability 0.86

Structure

x-ray diffraction · 4 distinct chains · 35% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.13)	protein	545	33% helix, 24% strand	P04585
B	P51 rt	protein	388	37% helix, 22% strand	P04585
P	DNA primer 20-mer	dna	18	—	—
T	DNA template 27-mer	dna	23	—	—

Ligands and binding sites

1RY · [[(2R,5S)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate · ligand · chains A, P, T
MG · Magnesium ion · metal · 2 copies · chains A, T
SO4 · Sulfate ion · ion · 3 copies · chains A, B, P, T

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

Pockets

12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	867	0.86	0.88	88	empty
2	933	0.85	0.86	95	empty
3	517	0.69	0.79	50	empty
4	412	0.68	0.80	41	empty
5	275	0.61	0.79	30	empty

Interfaces

6 interfaces between chains.

A–B · 3011 Å² buried · 30 hydrogen bonds · protein-protein
A–T · 1181 Å² buried · 10 hydrogen bonds · protein-nucleic
A–P · 890 Å² buried · 9 hydrogen bonds · protein-nucleic
P–T · 823 Å² buried · 60 hydrogen bonds · nucleic-nucleic
B–P · 109 Å² buried · 0 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

6OR7 · Structure of HIV-1 Reverse Transcriptase (RT) in complex with DNA AND (-)FTC-TP · 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 P04585
Elsewhere: RCSB PDB 6OR7 · PDBe 6OR7 · UniProt P04585

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