MolNFT v1 · #112516 · protein
Crystal structure of SGCC5 protein from streptomyces globisporus (apo form)
4ZNM · C-domain type II peptide synthetase: “Crystal structure of SGCC5 protein from streptomyces globisporus (apo form)”. X-ray diffraction, 2 ligands (NA, CL), 12 pockets (best druggability 0.86). MolNFT v1 #112516 on GenesisL1: 3D…
- PDB
- 4ZNM
- Type
- protein
- Length
- 887 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-domain type II peptide synthetase
- UniProt
- Q8GMG2
- Ligands
- NA, CL
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C-domain type II peptide synthetase | protein | 443 | 38% helix, 23% strand | Q8GMG2 |
| B | C-domain type II peptide synthetase | protein | 444 | 38% helix, 24% strand | Q8GMG2 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 371 | 0.86 | 0.95 | 50 | CL |
| 2 | 562 | 0.84 | 0.90 | 74 | CL |
| 3 | 722 | 0.73 | 0.79 | 68 | NA |
| 4 | 218 | 0.62 | 0.82 | 34 | empty |
| 5 | 56 | 0.61 | 0.92 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 661 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered, oxidation).
Compared structures
- 4ZNM · Crystal structure of SgcC5 protein from Streptomyces globisporus (apo form) · 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 Q8GMG2
- Elsewhere: RCSB PDB 4ZNM · PDBe 4ZNM · UniProt Q8GMG2
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