Research workbench
Heme D1 biosynthesis associated protein nirf in complex with dihydro- heme D1
Analyse Heme D1 biosynthesis associated protein nirf in complex with dihydro- heme D1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TV9
- Type
- protein
- Length
- 2,976 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein NIRF,PROTEIN nirf
- UniProt
- Q51480
- Ligands
- DHE
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Protein NIRF,PROTEIN nirf | protein | 372 | 5% helix, 49% strand | Q51480 |
Ligands and binding sites
- DHE · Heme D · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1155 | 0.84 | 0.85 | 104 | DHE |
| 2 | 709 | 0.84 | 0.88 | 77 | DHE |
| 3 | 698 | 0.84 | 0.88 | 74 | DHE |
| 4 | 1187 | 0.84 | 0.85 | 90 | DHE |
| 5 | 517 | 0.83 | 0.90 | 70 | DHE |
Interfaces
11 interfaces between chains.
- B–E · 2176 Ų buried · 47 hydrogen bonds · protein-protein
- C–G · 2088 Ų buried · 54 hydrogen bonds · protein-protein
- D–F · 633 Ų buried · 13 hydrogen bonds · protein-protein
- A–H · 578 Ų buried · 10 hydrogen bonds · protein-protein
- B–G · 503 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6TV9 · Heme d1 biosynthesis associated Protein NirF in complex with dihydro-heme d1 · the same entry in another collection · chain H against H, TM-score 1.00
- Q51480 · AlphaFold monomer V2.0 prediction for protein nirf (Q51480) · a predicted model of the same protein · chain A 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 Q51480
- Elsewhere: RCSB PDB 6TV9 · PDBe 6TV9 · UniProt Q51480
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