MolNFT v1 · #129654 · protein + DNA
Crystal structure of the S. cerevisiae condensin YCG1-BRN1 subcomplex bound to DNA (crystal form I)
5OQP · Condensin complex subunit 3: “Crystal structure of the S. cerevisiae condensin YCG1-BRN1 subcomplex bound to DNA (crystal form I)”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.72). MolNFT v1 #129654 on…
- PDB
- 5OQP
- Type
- protein + DNA
- Length
- 938 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
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 69% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Condensin complex subunit 3 | protein | 806 | 74% helix, 0% strand | Q06680 |
| B | Condensin complex subunit 2 | protein | 96 | 24% helix, 4% 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1013 | 0.72 | 0.76 | 70 | empty |
| 2 | 559 | 0.70 | 0.80 | 49 | empty |
| 3 | 100 | 0.45 | 0.79 | 14 | empty |
| 4 | 56 | 0.42 | 0.82 | 20 | empty |
| 5 | 125 | 0.38 | 0.74 | 21 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3937 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 819 Ų buried · 75 hydrogen bonds · nucleic-nucleic
- A–D · 423 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–C · 228 Ų buried · 0 hydrogen bonds · protein-nucleic
- B–C · 78 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 5OQP · 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 0.96
- 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 0.83
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 5OQP · PDBe 5OQP · UniProt Q06680 · UniProt P38170
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