MolNFT v1 · #174999 · protein
Crystal structure of the S103F mutant of bacillus subtilis (natto) yabj protein.
7CD2: “Crystal structure of the S103F mutant of bacillus subtilis (natto) yabj protein.”. X-ray diffraction, 19 pockets (best druggability 0.83). MolNFT v1 #174999 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.