Research workbench
Crystal structure of a marine metagenome trap solute binding protein specific for aromatic acid ligands (sorcerer II global ocean sampling expedition, unidentified microbe, locus tag GOS_1523157) in complex with co-crystallized 3-hydroxybenzoate
Analyse Crystal structure of a marine metagenome trap solute binding protein specific… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I7I
- Type
- protein
- Length
- 638 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trap solute binding protein
- Ligands
- 3HB
- Pockets
- 8 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trap solute binding protein | protein | 318 | 51% helix, 19% strand | — |
| B | Trap solute binding protein | protein | 320 | 51% helix, 18% strand | — |
Ligands and binding sites
- 3HB · 3-hydroxybenzoic acid · ligand · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 284 | 0.64 | 0.81 | 42 | PEG |
| 2 | 171 | 0.60 | 0.83 | 29 | empty |
| 3 | 241 | 0.58 | 0.79 | 33 | empty |
| 4 | 67 | 0.51 | 0.86 | 22 | empty |
| 5 | 98 | 0.36 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 521 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5I7I · Crystal structure of a marine metagenome TRAP solute binding protein specific for… · 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
- Elsewhere: RCSB PDB 5I7I · PDBe 5I7I
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