MolNFT v1 · #61206 · protein
The structure of CT381, the arginine binding protein from the periplasm chlamydia trachomatis
3DEL: “The structure of CT381, the arginine binding protein from the periplasm chlamydia trachomatis”. X-ray diffraction, 8 pockets (best druggability 0.73). MolNFT v1 #61206 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3DEL
- Type
- protein
- Length
- 928 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginine binding protein
- UniProt
- O84385
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C, D, F | Arginine binding protein | protein | 232 | 37% helix, 30% strand | O84385 |
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 860 | 0.73 | 0.77 | 64 | empty |
| 2 | 142 | 0.70 | 0.90 | 25 | empty |
| 3 | 450 | 0.57 | 0.73 | 37 | empty |
| 4 | 150 | 0.53 | 0.80 | 28 | empty |
| 5 | 187 | 0.53 | 0.78 | 25 | empty |
Interfaces
5 interfaces between chains.
- C–F · 1419 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 331 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 142 Ų buried · 2 hydrogen bonds · protein-protein
- B–F · 141 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 45 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3DEL · The structure of CT381, the arginine binding protein from the periplasm Chlamydia… · the same entry in another collection · chain F against F, TM-score 1.00
- O84385 · AlphaFold monomer V2.0 prediction for probable ABC transporter arginine-binding protein… · a predicted model of the same protein · chain F against A, TM-score 0.63
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 O84385
- Elsewhere: RCSB PDB 3DEL · PDBe 3DEL · UniProt O84385
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