MolNFT v1 · #79741 · protein
Crystal structure of E. COLI oppa complexed with endogenous ligands
3TCF · Periplasmic oligopeptide-binding protein: “Crystal structure of E. COLI oppa complexed with endogenous ligands”. X-ray diffraction, 20 pockets (best druggability 0.81). MolNFT v1 #79741 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3TCF
- Type
- protein
- Length
- 4,160 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic oligopeptide-binding protein; Endogenous peptide
- UniProt
- P23843
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Periplasmic oligopeptide-binding protein | protein | 517 | 35% helix, 22% strand | P23843 |
| I, J, K, L, M, N, O, P | Endogenous peptide | protein | 3 | 0% helix, 33% strand | — |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1163 | 0.81 | 0.82 | 92 | empty |
| 2 | 162 | 0.78 | 0.94 | 39 | empty |
| 3 | 177 | 0.77 | 0.93 | 40 | empty |
| 4 | 186 | 0.76 | 0.92 | 41 | empty |
| 5 | 185 | 0.75 | 0.91 | 42 | empty |
Interfaces
20 interfaces between chains.
- A–F · 823 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 817 Ų buried · 14 hydrogen bonds · protein-protein
- E–G · 815 Ų buried · 12 hydrogen bonds · protein-protein
- F–H · 788 Ų buried · 10 hydrogen bonds · protein-protein
- D–L · 297 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3TCF · Crystal structure of E. coli OppA complexed with endogenous ligands · the same entry in another collection · chain P against P, 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 P23843
- Elsewhere: RCSB PDB 3TCF · PDBe 3TCF · UniProt P23843
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