Research workbench
Cryo-EM structure of clamped S.CEREVISIAE condensin-DNA complex (form II)
Analyse Cryo-EM structure of clamped S.CEREVISIAE condensin-DNA complex (form II) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Q2Y
- Type
- protein + DNA
- Length
- 2,132 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Structural maintenance of chromosomes protein 2; Structural maintenance of chromosomes…
- UniProt
- P38989, Q12267, P38170, Q06156
- Ligands
- ADP, BEF, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 6 distinct chains · 60% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Structural maintenance of chromosomes protein 2 | protein | 431 | 46% helix, 18% strand | P38989 |
| B | Structural maintenance of chromosomes protein 4 | protein | 388 | 37% helix, 25% strand | Q12267 |
| C | Condensin complex subunit 2 | protein | 281 | 54% helix, 6% strand | P38170 |
| D | Condensin complex subunit 1 | protein | 976 | 77% helix, 0% strand | Q06156 |
| F | DNA (28-mer) | dna | 28 | — | — |
| G | DNA (28-mer) | dna | 28 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- BEF · Beryllium trifluoride ion · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
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 | 953 | 0.85 | 0.86 | 99 | empty |
| 2 | 864 | 0.82 | 0.84 | 77 | empty |
| 3 | 161 | 0.77 | 0.94 | 36 | ADP, BEF |
| 4 | 1090 | 0.77 | 0.79 | 85 | empty |
| 5 | 255 | 0.75 | 0.89 | 37 | ADP, BEF, MG |
Interfaces
14 interfaces between chains.
- C–D · 4734 Ų buried · 41 hydrogen bonds · protein-protein
- A–C · 2630 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1522 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1331 Ų buried · 12 hydrogen bonds · protein-protein
- F–G · 1165 Ų buried · 56 hydrogen bonds · nucleic-nucleic
Compared structures
- 7Q2Y · Cryo-EM structure of clamped S.cerevisiae condensin-DNA complex (form II) · the same entry in another collection · chain G against G, 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 0.94
- 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 0.74
- 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 0.37
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 P38989
- Every structure of UniProt Q12267
- Every structure of UniProt P38170
- Every structure of UniProt Q06156
- Elsewhere: RCSB PDB 7Q2Y · PDBe 7Q2Y · UniProt P38989 · UniProt Q12267 · UniProt P38170 · UniProt Q06156
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