MolNFT v1 · #143068 · protein
Crystal structure of an N-hydroxythienopyrimidine-2,4-dione RNase H active site inhibitor with multiple binding modes to HIV reverse transcriptase
6AOC · Reverse TRANSCRIPTASE/RIBONUCLEASE H: “Crystal structure of an N-hydroxythienopyrimidine-2,4-dione RNase H active site inhibitor with multiple…”. X-ray diffraction, 2 ligands (ZW2, MN), 20 pockets (best druggability 0.84). MolNFT v1…
- PDB
- 6AOC
- Type
- protein
- Length
- 1,953 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H; P51 rt
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.13
- UniProt
- P03366
- Ligands
- ZW2, MN
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 22% 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 | 555 | 32% helix, 23% strand | P03366 |
| B | P51 rt | protein | 425 | 35% helix, 19% strand | P03366 |
| C | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.13) | protein | 557 | 32% helix, 24% strand | P03366 |
| D | P51 rt | protein | 416 | 38% helix, 20% strand | P03366 |
Ligands and binding sites
- ZW2 · 6-benzyl-3-hydroxythieno[2,3-d]pyrimidine-2,4(1H,3H)-dione · ligand · 2 copies · chains A, C
- MN · Manganese (II) ion · metal · 4 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 68 copies · chains A, C, B, D
- PGE · Triethylene glycol · additive · 7 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 923 | 0.84 | 0.85 | 117 | EDO |
| 2 | 492 | 0.74 | 0.82 | 42 | PGE, EDO |
| 3 | 1077 | 0.74 | 0.77 | 102 | EDO |
| 4 | 1053 | 0.73 | 0.76 | 110 | empty |
| 5 | 471 | 0.71 | 0.81 | 36 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2844 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2787 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 612 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 483 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6AOC · Crystal Structure of an N-Hydroxythienopyrimidine-2,4-dione RNase H Active Site Inhibitor… · 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 P03366
- Elsewhere: RCSB PDB 6AOC · PDBe 6AOC · UniProt P03366
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