MolNFT v1 · #83621 · protein
Crystal structure of yidc from bacillus halodurans (form II)
3WO7 · Membrane protein insertase yidc 2: “Crystal structure of yidc from bacillus halodurans (form II)”. X-ray diffraction, 1 ligand (CU), 2 pockets (best druggability 0.77). MolNFT v1 #83621 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3WO7
- Type
- protein
- Length
- 449 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Membrane protein insertase yidc 2
- UniProt
- Q9KDP2
- Ligands
- CU
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Membrane protein insertase yidc 2 | protein | 224 | 75% helix, 2% strand | Q9KDP2 |
| B | Membrane protein insertase yidc 2 | protein | 225 | 76% helix, 2% strand | Q9KDP2 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 762 | 0.77 | 0.81 | 64 | empty |
| 2 | 549 | 0.75 | 0.82 | 52 | empty |
Interfaces
1 interface between chains.
- A–B · 361 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3WO7 · Crystal structure of YidC from Bacillus halodurans (form II) · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KDP2 · AlphaFold monomer V2.0 prediction for membrane protein insertase yidc 2 (Q9KDP2) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 Q9KDP2
- Elsewhere: RCSB PDB 3WO7 · PDBe 3WO7 · UniProt Q9KDP2
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