MolNFT v1 · #100427 · protein
Crystal structure of troa-like periplasmic binding protein PERIPLA_BP_2 from xylanimonas cellulosilytica
4MX8: “Crystal structure of troa-like periplasmic binding protein PERIPLA_BP_2 from xylanimonas cellulosilytica”. X-ray diffraction, 20 pockets (best druggability 0.88). MolNFT v1 #100427 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4MX8
- Type
- protein
- Length
- 1,809 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic binding protein
- UniProt
- D1BRG9
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Periplasmic binding protein | protein | 302 | 44% helix, 21% strand | D1BRG9 |
| C, E, F | Periplasmic binding protein | protein | 301 | 45% helix, 21% strand | D1BRG9 |
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1150 | 0.88 | 0.89 | 145 | empty |
| 2 | 757 | 0.86 | 0.90 | 101 | empty |
| 3 | 500 | 0.81 | 0.88 | 80 | empty |
| 4 | 646 | 0.80 | 0.85 | 87 | empty |
| 5 | 50 | 0.67 | 0.96 | 19 | empty |
Interfaces
9 interfaces between chains.
- E–F · 1114 Ų buried · 13 hydrogen bonds · protein-protein
- C–E · 1108 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 1083 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 1022 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1013 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 4MX8 · Crystal Structure of TroA-like Periplasmic Binding Protein Peripla_BP_2 from Xylanimonas… · 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 D1BRG9
- Elsewhere: RCSB PDB 4MX8 · PDBe 4MX8 · UniProt D1BRG9
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