MolNFT v1 · #185786 · protein + DNA
S.C. condensin core in DNA- and ATP-bound state
7QEN · DNA (35-mer): “S.C. condensin core in DNA- and ATP-bound state”. Electron microscopy, 2 ligands (ATP, MG), 20 pockets (best druggability 0.86). MolNFT v1 #185786 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7QEN
- Type
- protein + DNA
- Length
- 2,295 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (35-mer); Structural maintenance of chromosomes protein 4; Structural maintenance of…
- UniProt
- Q12267, P38989, P38170, Q06156
- Ligands
- ATP, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 6 distinct chains · 57% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | DNA (35-mer) | dna | 35 | — | — |
| G | DNA (35-mer) | dna | 35 | — | — |
| B | Structural maintenance of chromosomes protein 4 | protein | 419 | 38% helix, 21% strand | Q12267 |
| A | Structural maintenance of chromosomes protein 2 | protein | 465 | 49% helix, 18% strand | P38989 |
| C | Condensin complex subunit 2 | protein | 291 | 47% helix, 6% strand | P38170 |
| D | Condensin complex subunit 1 | protein | 1050 | 71% helix, 0% strand | Q06156 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains B, A
- MG · Magnesium ion · metal · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 822 | 0.86 | 0.88 | 90 | ATP, MG |
| 2 | 782 | 0.80 | 0.84 | 68 | empty |
| 3 | 1143 | 0.80 | 0.81 | 99 | empty |
| 4 | 268 | 0.77 | 0.90 | 42 | ATP, MG |
| 5 | 455 | 0.76 | 0.85 | 63 | empty |
Interfaces
15 interfaces between chains.
- C–D · 5489 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 2549 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1700 Ų buried · 12 hydrogen bonds · protein-protein
- F–G · 1417 Ų buried · 80 hydrogen bonds · nucleic-nucleic
- B–D · 1224 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7QEN · S.c. Condensin core in DNA- and ATP-bound state · the same entry in another collection · chain D against D, TM-score 1.00
- Q06156 · AlphaFold monomer V2.0 prediction for condensin complex subunit 1 (Q06156) · a predicted model of the same protein · chain D against A, TM-score 0.95
- Q12267 · AlphaFold monomer V2.0 prediction for structural maintenance of chromosomes protein 4… · a predicted model of the same protein · chain B against A, TM-score 0.92
- P38989 · AlphaFold monomer V2.0 prediction for structural maintenance of chromosomes protein 2… · a predicted model of the same protein · chain A against A, TM-score 0.72
- P38170 · AlphaFold monomer V2.0 prediction for condensin complex subunit 2 (P38170) · a predicted model of the same protein · chain C against A, TM-score 0.38
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 Q12267
- Every structure of UniProt P38989
- Every structure of UniProt P38170
- Every structure of UniProt Q06156
- Elsewhere: RCSB PDB 7QEN · PDBe 7QEN · UniProt Q12267 · UniProt P38989 · UniProt P38170 · UniProt Q06156
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