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Crystal structure of the S103F mutant of bacillus subtilis (natto) yabj protein.
Analyse Crystal structure of the S103F mutant of bacillus subtilis (natto) yabj protein. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CD4
- Type
- protein
- Length
- 461 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yabj protein
- UniProt
- D4G3D4
- Ligands
- ZN, MG, CL
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yabj protein | protein | 124 | 28% helix, 27% strand | D4G3D4 |
| B, D | Yabj protein | protein | 108 | 32% helix, 31% strand | D4G3D4 |
| C | Yabj protein | protein | 121 | 29% helix, 26% strand | D4G3D4 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains B, A, C, D
- CL · Chloride ion · ion · 10 copies · chains A, D, B, C
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1170 | 0.81 | 0.82 | 121 | CL, BTB, MG |
| 2 | 63 | 0.44 | 0.82 | 18 | empty |
| 3 | 65 | 0.42 | 0.81 | 14 | empty |
| 4 | 52 | 0.36 | 0.79 | 10 | empty |
Interfaces
6 interfaces between chains.
- A–C · 618 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 615 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 589 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 572 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 542 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7CD4 · Crystal structure of the S103F mutant of Bacillus subtilis (natto) YabJ protein. · 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 D4G3D4
- Elsewhere: RCSB PDB 7CD4 · PDBe 7CD4 · UniProt D4G3D4
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