Research workbench
Crystal structure of the degp dodecamer with a model substrate
Analyse Crystal structure of the degp dodecamer with a model substrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OTP
- Type
- protein
- Length
- 2,375 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease do; Lysozyme C
- EC
- 3.4.21.-, 3.2.1.17
- UniProt
- P0C0V0, B8YK79
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 8 distinct chains · 17% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protease do (EC 3.4.21.-) | protein | 381 | 16% helix, 39% strand | P0C0V0 |
| B | Protease do (EC 3.4.21.-) | protein | 392 | 18% helix, 41% strand | P0C0V0 |
| C | Protease do (EC 3.4.21.-) | protein | 382 | 18% helix, 41% strand | P0C0V0 |
| D | Protease do (EC 3.4.21.-) | protein | 388 | 18% helix, 41% strand | P0C0V0 |
| E | Protease do (EC 3.4.21.-) | protein | 388 | 17% helix, 40% strand | P0C0V0 |
| F | Protease do (EC 3.4.21.-) | protein | 378 | 16% helix, 39% strand | P0C0V0 |
| G, H, J, K, L | Lysozyme C (EC 3.2.1.17) | protein | 10 | 0% helix, 50% strand | B8YK79 |
| I | Lysozyme C (EC 3.2.1.17) | protein | 16 | 0% helix, 31% strand | B8YK79 |
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 415 | 0.79 | 0.87 | 48 | empty |
| 2 | 438 | 0.78 | 0.87 | 48 | empty |
| 3 | 882 | 0.73 | 0.77 | 89 | empty |
| 4 | 789 | 0.70 | 0.76 | 75 | empty |
| 5 | 720 | 0.69 | 0.77 | 70 | empty |
Interfaces
17 interfaces between chains.
- D–F · 1137 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1133 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1127 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 1117 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1113 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3OTP · Crystal structure of the DegP dodecamer with a model substrate · the same entry in another collection · chain L against L, 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
- Every structure of UniProt B8YK79
- Elsewhere: RCSB PDB 3OTP · PDBe 3OTP · UniProt P0C0V0 · UniProt B8YK79
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