MolNFT v1 · #135520 · protein
Structure of TP228 para-amppnp-parb complex
5U1G: “Structure of TP228 para-amppnp-parb complex”. X-ray diffraction, 1 ligand (ANP), 9 pockets (best druggability 0.87). MolNFT v1 #135520 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5U1G
- Type
- protein
- Length
- 882 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Para; TP228 parb fragment
- Ligands
- ANP
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 7 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A | Para | protein | 211 | 41% helix, 18% strand | — |
| B | Para | protein | 210 | 46% helix, 16% strand | — |
| C | Para | protein | 209 | 44% helix, 15% strand | — |
| Y | TP228 parb fragment | protein | 9 | 56% helix, 0% strand | — |
| Z | TP228 parb fragment | protein | 7 | 71% helix, 0% strand | — |
| K | TP228 parb fragment | protein | 15 | 53% helix, 0% strand | — |
| R | TP228 parb fragment | protein | 10 | 40% helix, 0% strand | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains D, C, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 805 | 0.87 | 0.90 | 103 | ANP |
| 2 | 350 | 0.82 | 0.92 | 50 | ANP |
| 3 | 327 | 0.81 | 0.91 | 48 | ANP |
| 4 | 256 | 0.62 | 0.81 | 31 | empty |
| 5 | 246 | 0.61 | 0.80 | 35 | empty |
Interfaces
12 interfaces between chains.
- D–C · 1180 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 1099 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 765 Ų buried · 11 hydrogen bonds · protein-protein
- D–A · 715 Ų buried · 11 hydrogen bonds · protein-protein
- D–K · 504 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5U1G · Structure of TP228 ParA-AMPPNP-ParB complex · the same entry in another collection · chain D against D, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 5U1G · PDBe 5U1G
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