Research workbench
Crystal structure of a periplasmic heme binding protein from shigella dysenteriae
Analyse Crystal structure of a periplasmic heme binding protein from shigella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R7A
- Type
- protein
- Length
- 1,021 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacterial heme binding protein
- UniProt
- O70018
- Ligands
- HEM
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Bacterial heme binding protein | protein | 255 | 45% helix, 17% strand | O70018 |
| B | Bacterial heme binding protein | protein | 256 | 45% helix, 18% strand | O70018 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1084 | 0.81 | 0.82 | 142 | empty |
| 2 | 461 | 0.71 | 0.81 | 56 | empty |
| 3 | 268 | 0.70 | 0.85 | 57 | HEM |
| 4 | 321 | 0.69 | 0.83 | 47 | empty |
| 5 | 81 | 0.47 | 0.82 | 24 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1138 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1125 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 672 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 152 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 17 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2R7A · Crystal Structure of a Periplasmic Heme Binding Protein from Shigella dysenteriae · 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 O70018
- Elsewhere: RCSB PDB 2R7A · PDBe 2R7A · UniProt O70018
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