Research workbench
HIV-1 reverse TRANSCRIPTASE/FRAGMENT of Fab 28/DNA complex
Analyse HIV-1 reverse TRANSCRIPTASE/FRAGMENT of Fab 28/DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HMI
- Type
- protein + DNA
- Length
- 1,459 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*AP*TP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*C)-3'); DNA (5'…
- EC
- 2.7.7.49
- UniProt
- P03366
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 24% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | DNA (5'- D(*AP*TP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*C)-3') | dna | 19 | — | — |
| F | DNA (5'- D(*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*CP*GP*CP*CP*A)-3') | dna | 18 | — | — |
| A | Subunit of V-1 reverse transcriptase (EC 2.7.7.49) | protein | 558 | 31% helix, 22% strand | P03366 |
| B | Hisubunit of V-1 reverse transcriptase (EC 2.7.7.49) | protein | 430 | 32% helix, 17% strand | P03366 |
| C | Fab fragment of monoclonal antibody 28 | protein | 214 | 5% helix, 50% strand | — |
| D | Fab fragment of monoclonal antibody 28 | protein | 220 | 7% helix, 51% strand | — |
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1000 | 0.83 | 0.84 | 82 | empty |
| 2 | 910 | 0.82 | 0.84 | 86 | empty |
| 3 | 962 | 0.78 | 0.80 | 71 | empty |
| 4 | 527 | 0.71 | 0.80 | 60 | empty |
| 5 | 429 | 0.67 | 0.79 | 41 | empty |
Interfaces
9 interfaces between chains.
- A–B · 2879 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 1936 Ų buried · 14 hydrogen bonds · protein-protein
- F–A · 847 Ų buried · 8 hydrogen bonds · protein-nucleic
- E–F · 841 Ų buried · 66 hydrogen bonds · nucleic-nucleic
- E–A · 789 Ų buried · 8 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2HMI · HIV-1 reverse TRANSCRIPTASE/FRAGMENT of Fab 28/DNA complex · the same entry in another collection · chain E against E, 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 2HMI · PDBe 2HMI · UniProt P03366
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