MolNFT v1 · #84314 · protein
Functional and structural role of the N-terminal extension in methanosarcina acetivorans protoglobin
3ZH0: “Functional and structural role of the N-terminal extension in methanosarcina acetivorans protoglobin”. X-ray diffraction, 1 ligand (HEM), 5 pockets (best druggability 0.85). MolNFT v1 #84314 on GenesisL1: 3D structure, binding sites…
- PDB
- 3ZH0
- Type
- protein
- Length
- 704 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protoglobin
- UniProt
- Q8TLY9
- Ligands
- HEM
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 68% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Protoglobin | protein | 176 | 68% helix, 2% strand | Q8TLY9 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D
- FMT · Formic acid · additive · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.85 | 0.94 | 35 | HEM, FMT |
| 2 | 338 | 0.84 | 0.93 | 40 | HEM, FMT |
| 3 | 462 | 0.83 | 0.90 | 50 | HEM, FMT |
| 4 | 444 | 0.82 | 0.89 | 47 | HEM, FMT, GOL |
| 5 | 247 | 0.57 | 0.78 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1989 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1967 Ų buried · 34 hydrogen bonds · protein-protein
- A–D · 672 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3ZH0 · Functional and structural role of the N-terminal extension in Methanosarcina acetivorans… · 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 Q8TLY9
- Elsewhere: RCSB PDB 3ZH0 · PDBe 3ZH0 · UniProt Q8TLY9
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