MolNFT v1 · #129653 · protein + DNA
Crystal structure of the S. cerevisiae condensin YCG1-BRN1 subcomplex bound to DNA (crystal form II)
5OQO · Condensin complex subunit 3: “Crystal structure of the S. cerevisiae condensin YCG1-BRN1 subcomplex bound to DNA (crystal form II)”. X-ray diffraction, 10 pockets (best druggability 0.76). MolNFT v1 #129653 on GenesisL1: 3D…
- PDB
- 5OQO
- Type
- protein + DNA
- Length
- 951 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Condensin complex subunit 3; Condensin complex subunit 2; DNA (5'…
- UniProt
- Q06680, P38170
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 68% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Condensin complex subunit 3 | protein | 817 | 72% helix, 1% strand | Q06680 |
| B | Condensin complex subunit 2 | protein | 98 | 30% helix, 3% strand | P38170 |
| C, D | DNA (5'- D(*GP*AP*TP*GP*TP*GP*TP*AP*GP*CP*TP*AP*CP*AP*CP*AP*TP*C)-3') | dna | 18 | — | — |
Ligands and binding sites
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1124 | 0.76 | 0.79 | 86 | empty |
| 2 | 126 | 0.52 | 0.80 | 20 | empty |
| 3 | 63 | 0.51 | 0.85 | 18 | empty |
| 4 | 142 | 0.47 | 0.78 | 31 | empty |
| 5 | 72 | 0.47 | 0.82 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3851 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 810 Ų buried · 68 hydrogen bonds · nucleic-nucleic
- A–D · 304 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–C · 250 Ų buried · 2 hydrogen bonds · protein-nucleic
- B–C · 45 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
- 5OQO · Crystal structure of the S. cerevisiae condensin Ycg1-Brn1 subcomplex bound to DNA… · the same entry in another collection · chain A against A, 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 0.97
- 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 0.88
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 Q06680
- Every structure of UniProt P38170
- Elsewhere: RCSB PDB 5OQO · PDBe 5OQO · UniProt Q06680 · UniProt P38170
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