Research workbench
Cryo-EM structure of DEGP12/OMP
Analyse Cryo-EM structure of DEGP12/OMP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZLE
- Type
- protein
- Length
- 5,098 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease do; Outer membrane protein C
- EC
- 3.4.21.-
- UniProt
- P0C0V0, P06996
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 10% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F, G, H, I, J, K, L, M | Protease do (EC 3.4.21.-) | protein | 396 | 15% helix, 34% strand | P0C0V0 |
| D | Outer membrane protein C | protein | 346 | 4% helix, 58% strand | P06996 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 988 | 0.83 | 0.84 | 122 | empty |
| 2 | 580 | 0.82 | 0.88 | 64 | empty |
| 3 | 556 | 0.82 | 0.88 | 61 | empty |
| 4 | 578 | 0.82 | 0.87 | 58 | empty |
| 5 | 545 | 0.81 | 0.87 | 56 | empty |
Interfaces
38 interfaces between chains.
- F–I · 1977 Ų buried · 225 hydrogen bonds · protein-protein
- C–E · 1308 Ų buried · 125 hydrogen bonds · protein-protein
- A–L · 1090 Ų buried · 93 hydrogen bonds · protein-protein
- D–K · 1007 Ų buried · 71 hydrogen bonds · protein-protein
- A–D · 1005 Ų buried · 75 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 isopeptide (isopeptide).
Compared structures
- 2ZLE · Cryo-EM structure of DegP12/OMP · 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 P0C0V0
- Every structure of UniProt P06996
- Elsewhere: RCSB PDB 2ZLE · PDBe 2ZLE · UniProt P0C0V0 · UniProt P06996
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