MolNFT v1 · #84400 · protein
ILE(149)G11PHE mutation of M.ACETIVORANS protoglobin in complex with cyanide
3ZJM: “ILE(149)G11PHE mutation of M.ACETIVORANS protoglobin in complex with cyanide”. X-ray diffraction, 2 ligands (HEM, CYN), 6 pockets (best druggability 0.87). MolNFT v1 #84400 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3ZJM
- Type
- protein
- Length
- 573 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protoglobin
- UniProt
- Q8TLY9
- Ligands
- HEM, CYN
- Pockets
- 6 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 65% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Protoglobin | protein | 191 | 65% helix, 2% strand | Q8TLY9 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains A, B, C
- CYN · Cyanide ion · ion · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 3 copies · chains A, C
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 310 | 0.87 | 0.97 | 39 | HEM, CYN |
| 2 | 286 | 0.86 | 0.96 | 32 | HEM, CYN |
| 3 | 284 | 0.86 | 0.96 | 35 | HEM, CYN |
| 4 | 607 | 0.66 | 0.76 | 60 | EPE |
| 5 | 82 | 0.44 | 0.81 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1939 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 433 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3ZJM · Ile(149)G11Phe mutation of M.acetivorans protoglobin in complex with cyanide · 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 3ZJM · PDBe 3ZJM · UniProt Q8TLY9
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