MolNFT v1 · #106764 · protein
Mppa periplasmic murein tripeptide binding protein, unliganded open form
4TOZ · Periplasmic murein peptide-binding protein: “Mppa periplasmic murein tripeptide binding protein, unliganded open form”. X-ray diffraction, 10 pockets (best druggability 0.69). MolNFT v1 #106764 on GenesisL1: 3D structure, binding…
- PDB
- 4TOZ
- Type
- protein
- Length
- 1,030 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic murein peptide-binding protein
- UniProt
- P77348
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Periplasmic murein peptide-binding protein | protein | 515 | 34% helix, 21% strand | P77348 |
| B | Periplasmic murein peptide-binding protein | protein | 515 | 34% helix, 21% strand | P77348 |
Ligands and binding sites
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.69 | 0.96 | 17 | empty |
| 2 | 94 | 0.68 | 0.92 | 27 | empty |
| 3 | 419 | 0.62 | 0.77 | 47 | empty |
| 4 | 297 | 0.62 | 0.79 | 37 | empty |
| 5 | 145 | 0.45 | 0.76 | 18 | empty |
Compared structures
- 4TOZ · MppA Periplasmic Murein Tripeptide Binding Protein, Unliganded Open Form · the same entry in another collection · chain B against B, TM-score 1.00
- P77348 · AlphaFold monomer V2.0 prediction for periplasmic murein peptide- binding protein (P77348) · a predicted model of the same protein · chain A against A, TM-score 0.74
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 P77348
- Elsewhere: RCSB PDB 4TOZ · PDBe 4TOZ · UniProt P77348
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