Research workbench
Crystal structure of the degp dodecamer with a modulator
Analyse Crystal structure of the degp dodecamer with a modulator in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JJK
- Type
- protein
- Length
- 2,368 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic serine endoprotease degp; Cys-tyr-tyr-lys-ile
- EC
- 3.4.21.107
- UniProt
- P0C0V0
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 8 distinct chains · 16% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Periplasmic serine endoprotease degp (EC 3.4.21.107) | protein | 381 | 16% helix, 39% strand | P0C0V0 |
| B | Periplasmic serine endoprotease degp (EC 3.4.21.107) | protein | 392 | 15% helix, 40% strand | P0C0V0 |
| C | Periplasmic serine endoprotease degp (EC 3.4.21.107) | protein | 382 | 15% helix, 38% strand | P0C0V0 |
| D | Periplasmic serine endoprotease degp (EC 3.4.21.107) | protein | 388 | 15% helix, 37% strand | P0C0V0 |
| E | Periplasmic serine endoprotease degp (EC 3.4.21.107) | protein | 388 | 14% helix, 40% strand | P0C0V0 |
| F | Periplasmic serine endoprotease degp (EC 3.4.21.107) | protein | 379 | 17% helix, 39% strand | P0C0V0 |
| G, H, I, J, K, M, N, O, P, Q, R | Cys-tyr-tyr-lys-ile | protein | 5 | 0% helix, 60% strand | — |
| L | Cys-tyr-tyr-lys-ile | protein | 3 | 0% helix, 33% strand | — |
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 427 | 0.77 | 0.86 | 54 | empty |
| 2 | 393 | 0.77 | 0.86 | 53 | empty |
| 3 | 53 | 0.72 | 0.98 | 19 | empty |
| 4 | 767 | 0.70 | 0.77 | 72 | empty |
| 5 | 672 | 0.69 | 0.77 | 69 | empty |
Interfaces
23 interfaces between chains.
- A–C · 1176 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1170 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1169 Ų buried · 19 hydrogen bonds · protein-protein
- D–F · 1134 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1129 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6JJK · Crystal structure of the DegP dodecamer with a modulator · the same entry in another collection · chain R against R, 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 P0C0V0
- Elsewhere: RCSB PDB 6JJK · PDBe 6JJK · UniProt P0C0V0
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