Research workbench
Structure of apo aztd from citrobacter koseri
Analyse Structure of apo aztd from citrobacter koseri in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N01
- Type
- protein
- Length
- 1,462 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aztd protein
- UniProt
- A8AF35
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 2% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Aztd protein | protein | 361 | 3% helix, 52% strand | A8AF35 |
| A | Aztd protein | protein | 367 | 2% helix, 52% strand | A8AF35 |
| C, D | Aztd protein | protein | 367 | 2% helix, 52% strand | A8AF35 |
Ligands and binding sites
- PGE · Triethylene glycol · additive · 2 copies · chains B, A
- EDO · 1,2-ethanediol · additive · 2 copies · chains C, D
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 941 | 0.81 | 0.83 | 80 | empty |
| 2 | 1158 | 0.80 | 0.82 | 90 | empty |
| 3 | 941 | 0.79 | 0.81 | 61 | empty |
| 4 | 895 | 0.78 | 0.81 | 56 | empty |
| 5 | 224 | 0.53 | 0.77 | 37 | empty |
Interfaces
3 interfaces between chains.
- A–D · 682 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 640 Ų buried · 6 hydrogen bonds · protein-protein
- B–A · 14 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6N01 · Structure of apo AztD from Citrobacter koseri · the same entry in another collection · chain B against B, 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 A8AF35
- Elsewhere: RCSB PDB 6N01 · PDBe 6N01 · UniProt A8AF35
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