Research workbench
Apo isdh-NEAT3 in space group P3121 at a resolution of 1.85 a
Analyse Apo isdh-NEAT3 in space group P3121 at a resolution of 1.85 a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VUA
- Type
- protein
- Length
- 683 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iron-regulated surface determinant protein H
- UniProt
- Q931P4
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 60% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iron-regulated surface determinant protein H | protein | 115 | 10% helix, 60% strand | Q931P4 |
| B, C, D | Iron-regulated surface determinant protein H | protein | 114 | 12% helix, 59% strand | Q931P4 |
| E, F | Iron-regulated surface determinant protein H | protein | 113 | 10% helix, 61% strand | Q931P4 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, C, E, F
- GOL · Glycerol · additive · 6 copies · chains B, C, E, F, D, A
- ACT · Acetate ion · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1090 | 0.82 | 0.83 | 121 | SO4, GOL |
| 2 | 75 | 0.75 | 0.98 | 23 | GOL |
| 3 | 51 | 0.33 | 0.78 | 13 | empty |
Interfaces
9 interfaces between chains.
- A–D · 594 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 586 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 583 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 577 Ų buried · 15 hydrogen bonds · protein-protein
- C–F · 475 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3VUA · Apo IsdH-NEAT3 in space group P3121 at a resolution of 1.85 A · the same entry in another collection · chain F against F, TM-score 1.00
- Q931P4 · AlphaFold monomer V2.0 prediction for iron-regulated surface determinant protein H… · a predicted model of the same protein · chain E against A, TM-score 0.95
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 Q931P4
- Elsewhere: RCSB PDB 3VUA · PDBe 3VUA · UniProt Q931P4
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