MolNFT v1 · #125126 · protein
Listeria monocytogenes oppa bound to peptide
5KZT · PEPTIDE/NICKEL transport system substrate-binding protein: “Listeria monocytogenes oppa bound to peptide”. X-ray diffraction, 11 pockets (best druggability 0.82). MolNFT v1 #125126 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5KZT
- Type
- protein
- Length
- 1,031 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PEPTIDE/NICKEL transport system substrate-binding protein; Hexamer peptide…
- UniProt
- A0A0H3GJB6
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PEPTIDE/NICKEL transport system substrate-binding protein | protein | 509 | 35% helix, 24% strand | A0A0H3GJB6 |
| B | PEPTIDE/NICKEL transport system substrate-binding protein | protein | 510 | 35% helix, 24% strand | A0A0H3GJB6 |
| C | Hexamer peptide: ser-asp-glu-ser-lys-gly | protein | 6 | 0% helix, 17% strand | — |
| D | Hexamer peptide: ser-asp-glu-ser-ser-gly | protein | 6 | 0% helix, 17% strand | — |
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 195 | 0.82 | 0.96 | 40 | empty |
| 2 | 190 | 0.81 | 0.96 | 40 | empty |
| 3 | 346 | 0.71 | 0.84 | 49 | empty |
| 4 | 370 | 0.70 | 0.82 | 54 | empty |
| 5 | 133 | 0.59 | 0.85 | 33 | empty |
Interfaces
3 interfaces between chains.
- A–C · 688 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 679 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 652 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5KZT · Listeria monocytogenes OppA bound to peptide · the same entry in another collection · chain A against A, 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
- Every structure of UniProt A0A0H3GJB6
- Elsewhere: RCSB PDB 5KZT · PDBe 5KZT · UniProt A0A0H3GJB6
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