Research workbench
Crystal structure of the protease + PDZ1 domain of degq from escherichia COLI
Analyse Crystal structure of the protease + PDZ1 domain of degq from escherichia COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3STJ
- Type
- protein
- Length
- 3,667 residues
- Chains
- 25
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease degq; Peptide (unk)
- EC
- 3.4.21.-
- UniProt
- P39099
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Protease degq (EC 3.4.21.-) | protein | 300 | 18% helix, 42% strand | P39099 |
| M, N, O, P, Q, R, S, T, U, V, W, X | Peptide (unk) | protein | 5 | 0% helix, 40% strand | — |
| Z | Peptide (unk) | protein | 7 | 0% helix, 29% strand | — |
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 901 | 0.75 | 0.79 | 104 | empty |
| 2 | 384 | 0.75 | 0.85 | 44 | empty |
| 3 | 390 | 0.75 | 0.85 | 44 | empty |
| 4 | 376 | 0.75 | 0.85 | 47 | empty |
| 5 | 813 | 0.74 | 0.79 | 91 | empty |
Interfaces
34 interfaces between chains.
- D–F · 1130 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1130 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1129 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1128 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1128 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3STJ · Crystal structure of the protease + PDZ1 domain of DegQ from Escherichia coli · the same entry in another collection · chain K against K, 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 P39099
- Elsewhere: RCSB PDB 3STJ · PDBe 3STJ · UniProt P39099
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