MolNFT v1 · #188509 · protein + DNA
ATP and DNA bound SMC5/6 core complex
7TVE · DNA (68-mer): “ATP and DNA bound SMC5/6 core complex”. Electron microscopy, 1 ligand (ATP), 20 pockets (best druggability 0.81). MolNFT v1 #188509 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7TVE
- Type
- protein + DNA
- Length
- 1,847 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (68-mer); DNA (78-mer); Non-structural maintenance of chromosomes element 1…
- EC
- 2.3.2.27
- UniProt
- A0A7I9FFW3, Q12749, Q08204, Q05541, P43124
- Ligands
- ATP
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 7 distinct chains · 40% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (68-mer) | dna | 27 | — | — |
| B | DNA (78-mer) | dna | 27 | — | — |
| C | Non-structural maintenance of chromosomes element 1 (EC 2.3.2.27) | protein | 310 | 40% helix, 10% strand | A0A7I9FFW3 |
| D | Structural maintenance of chromosomes protein 6 | protein | 445 | 44% helix, 14% strand | Q12749 |
| E | Structural maintenance of chromosomes protein 5 | protein | 461 | 37% helix, 14% strand | Q08204 |
| F | Non-structural maintenance of chromosome element 3 | protein | 270 | 38% helix, 8% strand | Q05541 |
| G | Non-structural maintenance of chromosome element 4 | protein | 307 | 40% helix, 3% strand | P43124 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 806 | 0.81 | 0.84 | 89 | ATP |
| 2 | 917 | 0.80 | 0.82 | 109 | empty |
| 3 | 166 | 0.79 | 0.95 | 36 | empty |
| 4 | 979 | 0.74 | 0.78 | 102 | empty |
| 5 | 427 | 0.72 | 0.83 | 48 | empty |
Interfaces
17 interfaces between chains.
- F–G · 3369 Ų buried · 25 hydrogen bonds · protein-protein
- D–G · 2975 Ų buried · 25 hydrogen bonds · protein-protein
- C–F · 2823 Ų buried · 31 hydrogen bonds · protein-protein
- E–G · 2254 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 1141 Ų buried · 79 hydrogen bonds · nucleic-nucleic
Compared structures
- 7TVE · ATP and DNA bound SMC5/6 core complex · the same entry in another collection · chain G against G, TM-score 1.00
- Q05541 · AlphaFold monomer V2.0 prediction for non-structural maintenance of chromosome element 3… · a predicted model of the same protein · chain F against A, TM-score 0.89
- Q08204 · AlphaFold monomer V2.0 prediction for structural maintenance of chromosomes protein 5… · a predicted model of the same protein · chain E against A, TM-score 0.88
- Q12749 · AlphaFold monomer V2.0 prediction for structural maintenance of chromosomes protein 6… · a predicted model of the same protein · chain D against A, TM-score 0.86
- P43124 · AlphaFold monomer V2.0 prediction for non-structural maintenance of chromosome element 4… · a predicted model of the same protein · chain G against A, TM-score 0.35
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 A0A7I9FFW3
- Every structure of UniProt Q12749
- Every structure of UniProt Q08204
- Every structure of UniProt Q05541
- Every structure of UniProt P43124
- Elsewhere: RCSB PDB 7TVE · PDBe 7TVE · UniProt A0A7I9FFW3 · UniProt Q12749 · UniProt Q08204 · UniProt Q05541 · UniProt P43124
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