MolNFT v1 · #67789 · protein
Crystal structure of putative metallopeptidase (YP_676511.1) from mesorhizobium sp. BNC1 at 2.13 a resolution
3IUU: “Crystal structure of putative metallopeptidase (YP_676511.1) from mesorhizobium sp. BNC1 at 2.13 a resolution”. X-ray diffraction, 2 ligands (ZN, SO4), 4 pockets (best druggability 0.77). MolNFT v1 #67789 on GenesisL1: 3D structure…
- PDB
- 3IUU
- Type
- protein
- Length
- 494 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative metallopeptidase
- UniProt
- Q11B79
- Ligands
- ZN, SO4
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative metallopeptidase | protein | 494 | 31% helix, 27% strand | Q11B79 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · 11 copies · chains A
- PGE · Triethylene glycol · additive · 2 copies · chains A
- IMD · Imidazole · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 520 | 0.77 | 0.85 | 81 | ZN, IMD, SO4, PEG |
| 2 | 60 | 0.54 | 0.88 | 18 | empty |
| 3 | 103 | 0.39 | 0.76 | 26 | empty |
| 4 | 57 | 0.34 | 0.77 | 11 | empty |
Modifications
Observed in the structure: 11 modified (engineered).
Compared structures
- 3IUU · Crystal structure of Putative metallopeptidase (YP_676511.1) from MESORHIZOBIUM SP. BNC1… · 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 Q11B79
- Elsewhere: RCSB PDB 3IUU · PDBe 3IUU · UniProt Q11B79
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