MolNFT v1 · #124313 · protein + DNA
Structure of rep-DNA complex
5KBJ · Replication initiator a, N-terminal: “Structure of rep-DNA complex”. X-ray diffraction, 20 pockets (best druggability 0.83). MolNFT v1 #124313 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5KBJ
- Type
- protein + DNA
- Length
- 1,095 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replication initiator a, N-terminal; DNA (32-mer)
- UniProt
- D2JDC3
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F | Replication initiator a, N-terminal | protein | 130 | 48% helix, 12% strand | D2JDC3 |
| C | Replication initiator a, N-terminal | protein | 125 | 49% helix, 15% strand | D2JDC3 |
| H | Replication initiator a, N-terminal | protein | 127 | 43% helix, 16% strand | D2JDC3 |
| G | Replication initiator a, N-terminal | protein | 129 | 38% helix, 10% strand | D2JDC3 |
| R | DNA (32-mer) | dna | 32 | — | — |
| W | DNA (32-mer) | dna | 32 | — | — |
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1144 | 0.83 | 0.84 | 102 | empty |
| 2 | 438 | 0.77 | 0.86 | 52 | empty |
| 3 | 947 | 0.77 | 0.80 | 84 | empty |
| 4 | 393 | 0.77 | 0.87 | 54 | empty |
| 5 | 838 | 0.72 | 0.77 | 77 | empty |
Interfaces
24 interfaces between chains.
- A–B · 2187 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 2172 Ų buried · 30 hydrogen bonds · protein-protein
- F–G · 2016 Ų buried · 26 hydrogen bonds · protein-protein
- C–H · 1990 Ų buried · 22 hydrogen bonds · protein-protein
- R–W · 1384 Ų buried · 131 hydrogen bonds · nucleic-nucleic
Compared structures
- 5KBJ · Structure of Rep-DNA complex · 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 D2JDC3
- Elsewhere: RCSB PDB 5KBJ · PDBe 5KBJ · UniProt D2JDC3
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