Research workbench
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
- 7CD2
- Type
- protein
- Length
- 2,163 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yabj protein
- UniProt
- D4G3D4
- Pockets
- 19 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, G, L, M, P, S | Yabj protein | protein | 108 | 32% helix, 30% strand | D4G3D4 |
| C | Yabj protein | protein | 119 | 29% helix, 25% strand | D4G3D4 |
| E, F, H, I, K, N, O, Q, R, T | Yabj protein | protein | 107 | 32% helix, 31% strand | D4G3D4 |
| J | Yabj protein | protein | 110 | 33% helix, 30% strand | D4G3D4 |
Pockets
19 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1111 | 0.83 | 0.84 | 104 | empty |
| 2 | 1052 | 0.83 | 0.84 | 97 | empty |
| 3 | 1032 | 0.83 | 0.84 | 102 | empty |
| 4 | 1008 | 0.82 | 0.83 | 100 | empty |
| 5 | 982 | 0.82 | 0.83 | 97 | empty |
Interfaces
47 interfaces between chains.
- M–Q · 729 Ų buried · 13 hydrogen bonds · protein-protein
- Q–R · 687 Ų buried · 15 hydrogen bonds · protein-protein
- S–T · 685 Ų buried · 11 hydrogen bonds · protein-protein
- J–P · 683 Ų buried · 11 hydrogen bonds · protein-protein
- M–N · 679 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 7CD2 · 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 7CD2 · PDBe 7CD2 · UniProt D4G3D4
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