Research workbench
Crystal structure of a two-domain fragment of mmtv integrase
Analyse Crystal structure of a two-domain fragment of mmtv integrase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CZ2
- Type
- protein
- Length
- 1,090 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pol polyprotein
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.4, 2.7.7.-, 3.1.-.-
- UniProt
- P03365
- Ligands
- MG, ZN
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 10 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pol polyprotein (EC 2.7.7.49, 2.7.7.7, 3.1.26.4, 2.7.7.-, 3.1.-.-) | protein | 151 | 44% helix, 19% strand | P03365 |
| B | Pol polyprotein (EC 2.7.7.49, 2.7.7.7, 3.1.26.4, 2.7.7.-, 3.1.-.-) | protein | 142 | 46% helix, 20% strand | P03365 |
| C | Pol polyprotein (EC 2.7.7.49, 2.7.7.7, 3.1.26.4, 2.7.7.-, 3.1.-.-) | protein | 152 | 44% helix, 19% strand | P03365 |
| D | Pol polyprotein (EC 2.7.7.49, 2.7.7.7, 3.1.26.4, 2.7.7.-, 3.1.-.-) | protein | 139 | 45% helix, 20% strand | P03365 |
| E | Pol polyprotein (EC 2.7.7.49, 2.7.7.7, 3.1.26.4, 2.7.7.-, 3.1.-.-) | protein | 153 | 44% helix, 19% strand | P03365 |
| F | Pol polyprotein (EC 2.7.7.49, 2.7.7.7, 3.1.26.4, 2.7.7.-, 3.1.-.-) | protein | 115 | 47% helix, 17% strand | P03365 |
| G, J, L | Pol polyprotein (EC 2.7.7.49, 2.7.7.7, 3.1.26.4, 2.7.7.-, 3.1.-.-) | protein | 41 | 71% helix, 0% strand | P03365 |
| H | Pol polyprotein (EC 2.7.7.49, 2.7.7.7, 3.1.26.4, 2.7.7.-, 3.1.-.-) | protein | 40 | 70% helix, 0% strand | P03365 |
| I | Pol polyprotein (EC 2.7.7.49, 2.7.7.7, 3.1.26.4, 2.7.7.-, 3.1.-.-) | protein | 39 | 69% helix, 0% strand | P03365 |
| K | Pol polyprotein (EC 2.7.7.49, 2.7.7.7, 3.1.26.4, 2.7.7.-, 3.1.-.-) | protein | 36 | 56% helix, 0% strand | P03365 |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
- ZN · Zinc ion · metal · 6 copies · chains G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 328 | 0.77 | 0.88 | 38 | empty |
| 2 | 1044 | 0.73 | 0.76 | 84 | empty |
| 3 | 309 | 0.69 | 0.83 | 33 | empty |
| 4 | 765 | 0.69 | 0.76 | 63 | empty |
| 5 | 483 | 0.69 | 0.79 | 48 | empty |
Interfaces
20 interfaces between chains.
- A–B · 1174 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 985 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 878 Ų buried · 6 hydrogen bonds · protein-protein
- C–L · 541 Ų buried · 5 hydrogen bonds · protein-protein
- A–G · 530 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5CZ2 · Crystal structure of a two-domain fragment of MMTV integrase · 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 P03365
- Elsewhere: RCSB PDB 5CZ2 · PDBe 5CZ2 · UniProt P03365
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