Research workbench
Head segment of the S.CEREVISIAE condensin holocomplex in presence of ATP
Analyse Head segment of the S.CEREVISIAE condensin holocomplex in presence of ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YVD
- Type
- protein
- Length
- 1,760 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Condensin complex subunit 2; Condensin complex subunit 3; Structural maintenance of…
- UniProt
- P38170, Q06680, P38989, Q12267
- Pockets
- 18 · best druggability 0.81
Structure
electron microscopy · 4 distinct chains · 57% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Condensin complex subunit 2 | protein | 101 | 39% helix, 7% strand | P38170 |
| A | Condensin complex subunit 3 | protein | 799 | 74% helix, 0% strand | Q06680 |
| C | Structural maintenance of chromosomes protein 2 | protein | 446 | 44% helix, 10% strand | P38989 |
| D | Structural maintenance of chromosomes protein 4 | protein | 414 | 41% helix, 13% strand | Q12267 |
Pockets
18 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 951 | 0.81 | 0.83 | 138 | empty |
| 2 | 1106 | 0.78 | 0.80 | 124 | empty |
| 3 | 879 | 0.77 | 0.81 | 103 | empty |
| 4 | 793 | 0.76 | 0.81 | 96 | empty |
| 5 | 806 | 0.76 | 0.80 | 105 | empty |
Interfaces
5 interfaces between chains.
- C–D · 449 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 444 Ų buried · 2 hydrogen bonds · protein-protein
- B–A · 442 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 206 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 168 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6YVD · Head segment of the S.cerevisiae condensin holocomplex in presence of ATP · the same entry in another collection · chain D against D, TM-score 1.00
- Q06680 · AlphaFold monomer V2.0 prediction for condensin complex subunit 3 (Q06680) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q12267 · AlphaFold monomer V2.0 prediction for structural maintenance of chromosomes protein 4… · a predicted model of the same protein · chain D against A, TM-score 0.81
- P38989 · AlphaFold monomer V2.0 prediction for structural maintenance of chromosomes protein 2… · a predicted model of the same protein · chain C against A, TM-score 0.70
- P38170 · AlphaFold monomer V2.0 prediction for condensin complex subunit 2 (P38170) · a predicted model of the same protein · chain B against A, TM-score 0.63
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 P38170
- Every structure of UniProt Q06680
- Every structure of UniProt P38989
- Every structure of UniProt Q12267
- Elsewhere: RCSB PDB 6YVD · PDBe 6YVD · UniProt P38170 · UniProt Q06680 · UniProt P38989 · UniProt Q12267
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