MolNFT v1 · #107770 · protein + DNA
The complex of SPO0J and pars DNA in chromosomal partition system
4UMK · Probable chromosome-partitioning protein parb: “The complex of SPO0J and pars DNA in chromosomal partition system”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.81). MolNFT v1 #107770 on GenesisL1: 3D structure…
- PDB
- 4UMK
- Type
- protein + DNA
- Length
- 820 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable chromosome-partitioning protein parb; DNA
- UniProt
- O25758
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 51% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable chromosome-partitioning protein parb | protein | 172 | 59% helix, 6% strand | O25758 |
| B | Probable chromosome-partitioning protein parb | protein | 183 | 46% helix, 6% strand | O25758 |
| C | Probable chromosome-partitioning protein parb | protein | 193 | 48% helix, 0% strand | O25758 |
| D | Probable chromosome-partitioning protein parb | protein | 176 | 52% helix, 0% strand | O25758 |
| W, Z | DNA | dna | 24 | — | — |
| X, Y | DNA | dna | 24 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, X, B, C, D, W
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1193 | 0.81 | 0.82 | 126 | SO4 |
| 2 | 704 | 0.77 | 0.82 | 67 | empty |
| 3 | 488 | 0.75 | 0.84 | 54 | empty |
| 4 | 283 | 0.56 | 0.77 | 31 | empty |
| 5 | 164 | 0.56 | 0.81 | 29 | empty |
Interfaces
11 interfaces between chains.
- Y–Z · 1078 Ų buried · 120 hydrogen bonds · nucleic-nucleic
- W–X · 1066 Ų buried · 119 hydrogen bonds · nucleic-nucleic
- B–D · 863 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 811 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 636 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4UMK · The complex of Spo0J and parS DNA in chromosomal partition system · the same entry in another collection · chain Z against Z, TM-score 1.00
- O25758 · AlphaFold monomer V2.0 prediction for probable chromosome- partitioning protein parb… · a predicted model of the same protein · chain A against A, TM-score 0.65
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 O25758
- Elsewhere: RCSB PDB 4UMK · PDBe 4UMK · UniProt O25758
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