Research workbench
Crystal structure of an auxiliary nutrient binding protein (BACOVA_00264) from bacteroides ovatus atcc 8483 at 1.70 a resolution
Analyse Crystal structure of an auxiliary nutrient binding protein (BACOVA_00264) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HW6
- Type
- protein
- Length
- 1,694 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein, IPT/TIG domain protein
- UniProt
- A7LR39
- Ligands
- IOD, CL
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Hypothetical protein, IPT/TIG domain protein | protein | 424 | 4% helix, 47% strand | A7LR39 |
| B | Hypothetical protein, IPT/TIG domain protein | protein | 422 | 4% helix, 48% strand | A7LR39 |
Ligands and binding sites
- IOD · Iodide ion · ion · 12 copies · chains A, B, C, D
- CL · Chloride ion · ion · 10 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 713 | 0.78 | 0.83 | 91 | IOD, CL |
| 2 | 350 | 0.73 | 0.85 | 44 | empty |
| 3 | 397 | 0.72 | 0.83 | 35 | IOD |
| 4 | 331 | 0.72 | 0.85 | 35 | empty |
| 5 | 457 | 0.72 | 0.81 | 36 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1059 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1051 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 362 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 211 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 58 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 4HW6 · Crystal structure of an auxiliary nutrient binding protein (BACOVA_00264) from… · 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 A7LR39
- Elsewhere: RCSB PDB 4HW6 · PDBe 4HW6 · UniProt A7LR39
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