MolNFT v1 · #163609 · protein + DNA
Cutting state of the E. COLI MRE11-RAD50 (sbccd) head complex bound to ADP and dsdna.
6S85 · Nuclease sbccd subunit C: “Cutting state of the E. COLI MRE11-RAD50 (sbccd) head complex bound to ADP and dsdna.”. Electron microscopy, 3 ligands (ADP, MN, MG), 20 pockets (best druggability 0.81). MolNFT v1 #163609 on GenesisL1: 3D…
- PDB
- 6S85
- Type
- protein + DNA
- Length
- 1,549 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclease sbccd subunit C; Nuclease sbccd subunit D; DNA (31-mer); DNA (32-mer)
- UniProt
- A0A037YDI0, C3TMC7
- Ligands
- ADP, MN, MG
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 6 distinct chains · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Nuclease sbccd subunit C | protein | 374 | 34% helix, 17% strand | A0A037YDI0 |
| D | Nuclease sbccd subunit C | protein | 375 | 38% helix, 18% strand | A0A037YDI0 |
| A | Nuclease sbccd subunit D | protein | 381 | 32% helix, 21% strand | C3TMC7 |
| B | Nuclease sbccd subunit D | protein | 356 | 30% helix, 20% strand | C3TMC7 |
| E | DNA (31-mer) | dna | 31 | — | — |
| F | DNA (32-mer) | dna | 32 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, F, B
- MG · Magnesium ion · metal · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 648 | 0.81 | 0.86 | 81 | ADP, MG |
| 2 | 686 | 0.81 | 0.85 | 76 | empty |
| 3 | 601 | 0.76 | 0.83 | 54 | empty |
| 4 | 92 | 0.75 | 0.96 | 24 | empty |
| 5 | 300 | 0.74 | 0.87 | 29 | empty |
Interfaces
12 interfaces between chains.
- D–A · 1695 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1518 Ų buried · 15 hydrogen bonds · protein-protein
- C–B · 1487 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 1424 Ų buried · 110 hydrogen bonds · nucleic-nucleic
- A–B · 762 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6S85 · Cutting state of the E. coli Mre11-Rad50 (SbcCD) head complex bound to ADP and dsDNA. · the same entry in another collection · chain C against C, 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 A0A037YDI0
- Every structure of UniProt C3TMC7
- Elsewhere: RCSB PDB 6S85 · PDBe 6S85 · UniProt A0A037YDI0 · UniProt C3TMC7
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