MolNFT v1 · #158868 · protein + DNA
Crystal structure of CSM6 in complex with CDA4 by soaking CDA4 into CSM6
6O71: “Crystal structure of CSM6 in complex with CDA4 by soaking CDA4 into CSM6”. X-ray diffraction, 10 pockets (best druggability 0.87). MolNFT v1 #158868 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6O71
- Type
- protein + DNA
- Length
- 873 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CSM6; Cyclic DNA CDA4
- UniProt
- B6YWC3
- Pockets
- 10 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CSM6 | protein | 433 | 47% helix, 20% strand | B6YWC3 |
| B | CSM6 | protein | 432 | 47% helix, 20% strand | B6YWC3 |
| C, D | Cyclic DNA CDA4 | dna | 4 | — | — |
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 992 | 0.87 | 0.88 | 82 | empty |
| 2 | 266 | 0.82 | 0.94 | 40 | empty |
| 3 | 98 | 0.39 | 0.77 | 20 | empty |
| 4 | 73 | 0.39 | 0.78 | 11 | empty |
| 5 | 55 | 0.36 | 0.79 | 11 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2361 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 469 Ų buried · 4 hydrogen bonds · protein-nucleic
- A–D · 424 Ų buried · 4 hydrogen bonds · protein-nucleic
- A–C · 381 Ų buried · 4 hydrogen bonds · protein-nucleic
- B–C · 368 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 6O71 · Crystal structure of Csm6 in complex with cdA4 by soaking cdA4 into Csm6 · 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 B6YWC3
- Elsewhere: RCSB PDB 6O71 · PDBe 6O71 · UniProt B6YWC3
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