MolNFT v1 · #56388 · protein
Crystal structure of isdg-N7A in complex with hemin
2ZDO · Heme-degrading monooxygenase isdg: “Crystal structure of isdg-N7A in complex with hemin”. X-ray diffraction, 1 ligand (HEM), 5 pockets (best druggability 0.69). MolNFT v1 #56388 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2ZDO
- Type
- protein
- Length
- 433 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heme-degrading monooxygenase isdg
- EC
- 1.14.99.3
- UniProt
- Q7A649
- Ligands
- HEM
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Heme-degrading monooxygenase isdg (EC 1.14.99.3) | protein | 108 | 23% helix, 42% strand | Q7A649 |
| D | Heme-degrading monooxygenase isdg (EC 1.14.99.3) | protein | 109 | 24% helix, 41% strand | Q7A649 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.69 | 0.81 | 44 | HEM |
| 2 | 327 | 0.69 | 0.82 | 36 | HEM |
| 3 | 282 | 0.69 | 0.83 | 30 | HEM |
| 4 | 338 | 0.68 | 0.81 | 37 | HEM |
| 5 | 54 | 0.32 | 0.76 | 13 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1606 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1604 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 175 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 39 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 37 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2ZDO · Crystal structure of IsdG-N7A in complex with hemin · the same entry in another collection · chain A against A, TM-score 1.00
- Q7A649 · AlphaFold monomer V2.0 prediction for heme oxygenase (staphylobilin- producing) 1 (Q7A649) · 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 Q7A649
- Elsewhere: RCSB PDB 2ZDO · PDBe 2ZDO · UniProt Q7A649
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