MolNFT v1 · #168277 · protein + RNA

+3 extended HIV-1 reverse transcriptase initiation complex core (intermediate state)

6WB1 · HIV-1 viral RNA genome fragment: “+3 extended HIV-1 reverse transcriptase initiation complex core (intermediate state)”. Electron microscopy, 20 pockets (best druggability 0.82). MolNFT v1 #168277 on GenesisL1: 3D structure, binding…

PDB: 6WB1
Type: protein + RNA
Length: 1,019 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HIV-1 viral RNA genome fragment; TRNA lysine 3; Reverse TRANSCRIPTASE/RIBONUCLEASE H…
EC: 2.7.7.49, 2.7.7.7, 3.1.26.13
UniProt: P03366
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · 4 distinct chains · 34% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	HIV-1 viral RNA genome fragment	rna	33	—	—
D	TRNA lysine 3	rna	42	—	—
A	Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.13)	protein	542	31% helix, 14% strand	P03366
B	Reverse transcriptase P51 subunit	protein	402	38% helix, 13% strand	P03366

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	766	0.82	0.85	97	empty
2	532	0.81	0.87	68	empty
3	307	0.80	0.91	58	empty
4	365	0.79	0.89	42	empty
5	334	0.76	0.87	47	empty

Interfaces

6 interfaces between chains.

A–B · 2125 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 1335 Å² buried · 140 hydrogen bonds · nucleic-nucleic
C–A · 727 Å² buried · 5 hydrogen bonds · protein-nucleic
D–A · 412 Å² buried · 3 hydrogen bonds · protein-nucleic
D–B · 73 Å² buried · 0 hydrogen bonds · protein-nucleic

Compared structures

6WB1 · +3 extended HIV-1 reverse transcriptase initiation complex core (intermediate state) · the same entry in another collection · chain C against C, 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 P03366
Elsewhere: RCSB PDB 6WB1 · PDBe 6WB1 · UniProt P03366

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