Research workbench
Crystal structure of the lambda repressor
Analyse Crystal structure of the lambda repressor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BDN
- Type
- protein + DNA
- Length
- 506 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*DAP*DAP*DTP*DAP*DCP*DCP*DAP*DCP*DTP*DGP*DGP*DCP*DGP*DGP*DTP*DGP*DA…
- UniProt
- P03034
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (5'- D(*DAP*DAP*DTP*DAP*DCP*DCP*DAP*DCP*DTP*DGP*DGP*DCP*DGP*DGP*DTP*DGP*DA P*DTP*DAP*DT)-3') | dna | 19 | — | — |
| D | DNA (5'- D(*DTP*DAP*DTP*DAP*DTP*DCP*DAP*DCP*DCP*DGP*DCP*DCP*DAP*DGP*DTP*DGP*DG P*DTP*DAP*DT)-3') | dna | 19 | — | — |
| A, B | Lambda repressor | protein | 234 | 25% helix, 12% strand | P03034 |
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1179 | 0.80 | 0.82 | 120 | empty |
| 2 | 81 | 0.71 | 0.95 | 30 | empty |
| 3 | 247 | 0.68 | 0.84 | 37 | empty |
| 4 | 50 | 0.57 | 0.90 | 23 | empty |
| 5 | 119 | 0.57 | 0.84 | 22 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2390 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 759 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- D–A · 434 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–B · 420 Ų buried · 8 hydrogen bonds · protein-nucleic
- C–A · 366 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 3BDN · Crystal Structure of the Lambda Repressor · the same entry in another collection · chain B against B, 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 P03034
- Elsewhere: RCSB PDB 3BDN · PDBe 3BDN · UniProt P03034
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