Research workbench
Structure of a complex between hemopexin and hemopexin binding protein
Analyse Structure of a complex between hemopexin and hemopexin binding protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RT6
- Type
- protein
- Length
- 977 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HEME/HEMOPEXIN-binding protein; Hemopexin
- UniProt
- P44602, P20058
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HEME/HEMOPEXIN-binding protein | protein | 805 | 6% helix, 51% strand | P44602 |
| B | Hemopexin | protein | 172 | 4% helix, 42% strand | P20058 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 425 | 0.68 | 0.80 | 55 | empty |
| 2 | 181 | 0.56 | 0.80 | 29 | empty |
| 3 | 75 | 0.40 | 0.79 | 18 | empty |
| 4 | 126 | 0.40 | 0.74 | 20 | empty |
| 5 | 93 | 0.38 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1706 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4RT6 · Structure of a complex between hemopexin and hemopexin binding protein · the same entry in another collection · chain A against A, TM-score 1.00
- P44602 · AlphaFold monomer V2.0 prediction for HEME/HEMOPEXIN-binding protein (P44602) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P20058 · AlphaFold monomer V2.0 prediction for hemopexin (P20058) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P44602
- Every structure of UniProt P20058
- Elsewhere: RCSB PDB 4RT6 · PDBe 4RT6 · UniProt P44602 · UniProt P20058
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