Research workbench
Structure of heme transport protein isdh-NEAT3 from S. aureus in complex with indium-porphyrin
Analyse Structure of heme transport protein isdh-NEAT3 from S. aureus in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VTM
- Type
- protein
- Length
- 226 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iron-regulated surface determinant protein H
- UniProt
- Q931P4
- Ligands
- 3ZZ
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 61% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Iron-regulated surface determinant protein H | protein | 113 | 12% helix, 61% strand | Q931P4 |
Ligands and binding sites
- 3ZZ · Protoporphyrin IX containing indium · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 407 | 0.71 | 0.81 | 44 | 3ZZ |
| 2 | 56 | 0.36 | 0.79 | 11 | GOL |
Interfaces
1 interface between chains.
- A–B · 317 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3VTM · Structure of heme transport protein IsdH-NEAT3 from S. aureus in complex with… · the same entry in another collection · chain A against A, 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 A against A, TM-score 0.98
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 3VTM · PDBe 3VTM · UniProt Q931P4
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