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Crystal structure of a ybjq-like fold protein of unknown function (BH3498) from bacillus halodurans at 1.46 a resolution
Analyse Crystal structure of a ybjq-like fold protein of unknown function (BH3498) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VMF
- Type
- protein
- Length
- 407 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein
- UniProt
- Q9K772
- Ligands
- NA
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hypothetical protein | protein | 136 | 26% helix, 36% strand | Q9K772 |
| C | Hypothetical protein | protein | 135 | 26% helix, 36% strand | Q9K772 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A, B, C
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, C
- ACT · Acetate ion · additive · 2 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 94 | 0.75 | 0.98 | 25 | NA |
| 2 | 74 | 0.34 | 0.76 | 17 | ACT |
| 3 | 56 | 0.34 | 0.78 | 18 | empty |
| 4 | 89 | 0.32 | 0.73 | 17 | ACT |
| 5 | 62 | 0.30 | 0.75 | 17 | EDO, EPE |
Interfaces
3 interfaces between chains.
- B–C · 1351 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1343 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1307 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 1VMF · CRYSTAL STRUCTURE OF a YBJQ-LIKE FOLD PROTEIN OF UNKNOWN FUNCTION (BH3498) FROM BACILLUS… · 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 Q9K772
- Elsewhere: RCSB PDB 1VMF · PDBe 1VMF · UniProt Q9K772
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