MolNFT v1 · #116414 · protein
Structural studies of AAV2 REP68 reveal a partially structured linker and compact domain conformation
5DCX · Protein REP68: “Structural studies of AAV2 REP68 reveal a partially structured linker and compact domain conformation”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.77). MolNFT v1 #116414 on GenesisL1: 3D…
- PDB
- 5DCX
- Type
- protein
- Length
- 2,169 residues
- Chains
- 11
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein REP68
- EC
- 3.6.4.12
- UniProt
- P03132
- Ligands
- MG
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 10 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein REP68 (EC 3.6.4.12) | protein | 209 | 43% helix, 17% strand | P03132 |
| B | Protein REP68 (EC 3.6.4.12) | protein | 205 | 43% helix, 17% strand | P03132 |
| C | Protein REP68 (EC 3.6.4.12) | protein | 202 | 43% helix, 19% strand | P03132 |
| D | Protein REP68 (EC 3.6.4.12) | protein | 202 | 45% helix, 18% strand | P03132 |
| E | Protein REP68 (EC 3.6.4.12) | protein | 195 | 42% helix, 18% strand | P03132 |
| F | Protein REP68 (EC 3.6.4.12) | protein | 188 | 41% helix, 19% strand | P03132 |
| G | Protein REP68 (EC 3.6.4.12) | protein | 203 | 42% helix, 19% strand | P03132 |
| H | Protein REP68 (EC 3.6.4.12) | protein | 202 | 45% helix, 18% strand | P03132 |
| I, K | Protein REP68 (EC 3.6.4.12) | protein | 189 | 41% helix, 19% strand | P03132 |
| J | Protein REP68 (EC 3.6.4.12) | protein | 185 | 41% helix, 19% strand | P03132 |
Ligands and binding sites
- MG · Magnesium ion · metal · 11 copies · chains A, B, C, D, E, F, G, H, I, J, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 986 | 0.77 | 0.79 | 84 | empty |
| 2 | 880 | 0.74 | 0.78 | 71 | empty |
| 3 | 760 | 0.71 | 0.77 | 44 | empty |
| 4 | 502 | 0.68 | 0.79 | 37 | empty |
| 5 | 473 | 0.66 | 0.78 | 62 | empty |
Interfaces
19 interfaces between chains.
- C–D · 777 Ų buried · 12 hydrogen bonds · protein-protein
- G–J · 720 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 703 Ų buried · 10 hydrogen bonds · protein-protein
- B–J · 693 Ų buried · 13 hydrogen bonds · protein-protein
- B–E · 642 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5DCX · Structural studies of AAV2 Rep68 reveal a partially structured linker and compact domain… · 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 P03132
- Elsewhere: RCSB PDB 5DCX · PDBe 5DCX · UniProt P03132
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