MolNFT v1 · #110255 · protein + DNA
Escherichia COLI replication terminator protein (tus) complexed with DNA- GC(6) swapped.
4XR3 · DNA replication terminus site-binding protein: “Escherichia COLI replication terminator protein (tus) complexed with DNA- GC(6) swapped.”. X-ray diffraction, 1 ligand (IOD), 8 pockets (best druggability 0.69). MolNFT v1 #110255 on…
- PDB
- 4XR3
- Type
- protein + DNA
- Length
- 335 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA replication terminus site-binding protein; DNA…
- UniProt
- P16525
- Ligands
- IOD
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA replication terminus site-binding protein | protein | 305 | 38% helix, 26% strand | P16525 |
| B | DNA (5'-D(*TP*AP*GP*TP*TP*AP*CP*AP*AP*CP*AP*TP*AP*GP*T)- 3') | dna | 15 | — | — |
| C | DNA (5'-D(*TP*AP*CP*TP*AP*TP*GP*TP*TP*GP*TP*AP*AP*CP*TP*A)- 3') | dna | 15 | — | — |
Ligands and binding sites
- IOD · Iodide ion · ion · 4 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 543 | 0.69 | 0.79 | 36 | IOD |
| 2 | 228 | 0.62 | 0.82 | 36 | empty |
| 3 | 80 | 0.59 | 0.89 | 27 | empty |
| 4 | 115 | 0.45 | 0.79 | 15 | MPD |
| 5 | 108 | 0.43 | 0.78 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1550 Ų buried · 28 hydrogen bonds · protein-nucleic
- A–C · 1347 Ų buried · 20 hydrogen bonds · protein-nucleic
- B–C · 678 Ų buried · 55 hydrogen bonds · nucleic-nucleic
Compared structures
- 4XR3 · Escherichia Coli Replication Terminator Protein (Tus) Complexed With DNA- GC(6) swapped. · the same entry in another collection · chain B against B, TM-score 1.00
- P16525 · AlphaFold monomer V2.0 prediction for DNA replication terminus site- binding protein… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P16525
- Elsewhere: RCSB PDB 4XR3 · PDBe 4XR3 · UniProt P16525
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