Research workbench
Crystal structure of a lipocalin family protein (BACOVA_00364) from bacteroides ovatus atcc 8483 at 1.95 a resolution
Analyse Crystal structure of a lipocalin family protein (BACOVA_00364) from bacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GZV
- Type
- protein
- Length
- 1,084 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein
- UniProt
- A7LRD6
- Ligands
- UNL, NA
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 3% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein | protein | 139 | 4% helix, 58% strand | A7LRD6 |
| B, D | Hypothetical protein | protein | 133 | 2% helix, 61% strand | A7LRD6 |
| C, F, G | Hypothetical protein | protein | 136 | 2% helix, 60% strand | A7LRD6 |
| E | Hypothetical protein | protein | 141 | 2% helix, 57% strand | A7LRD6 |
| H | Hypothetical protein | protein | 130 | 2% helix, 58% strand | A7LRD6 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 5 copies · chains A, C, B, D, E, G, F, H
- NA · Sodium ion · metal · chains F
- GOL · Glycerol · additive · 4 copies · chains B, C, E, H
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1027 | 0.80 | 0.82 | 87 | empty |
| 2 | 1185 | 0.80 | 0.81 | 103 | empty |
| 3 | 365 | 0.64 | 0.79 | 39 | empty |
| 4 | 305 | 0.60 | 0.78 | 35 | empty |
| 5 | 284 | 0.58 | 0.78 | 36 | empty |
Interfaces
14 interfaces between chains.
- E–G · 1988 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1979 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 1950 Ų buried · 19 hydrogen bonds · protein-protein
- F–H · 1938 Ų buried · 20 hydrogen bonds · protein-protein
- F–G · 607 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 4GZV · Crystal structure of a lipocalin family protein (BACOVA_00364) from Bacteroides ovatus… · 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 A7LRD6
- Elsewhere: RCSB PDB 4GZV · PDBe 4GZV · UniProt A7LRD6
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