MolNFT v1 · #55315 · protein
Methanobactin HM1
2YGI: “Methanobactin HM1”. X-ray diffraction, 3 ligands (HM7, HM8, CU). MolNFT v1 #55315 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2YGI
- Type
- protein
- Length
- 16 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methanobactin HM1
- Ligands
- HM7, HM8, CU
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Methanobactin HM1 | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- HM7 · 3-methylthioethane-pyrazinedione · ligand · 4 copies · chains A, C, B, D
- HM8 · 2-[(1S,2R)-1-amino-2-(sulfooxy)propyl]-5-hydroxy-1,3-oxazole-4-carbothioic O-acid · ligand · 4 copies · chains A, B, C, D
- CU · Copper (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
3 interfaces between chains.
- B–D · 79 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 76 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 64 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 covalent (covalent ligand).
Compared structures
- 2YGI · Methanobactin HM1 · 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
- Elsewhere: RCSB PDB 2YGI · PDBe 2YGI
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