Research workbench
Mepa, active form with zn in P1
Analyse Mepa, active form with zn in P1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1U10
- Type
- protein
- Length
- 1,434 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-insensitive murein endopeptidase
- EC
- 3.4.99.-
- UniProt
- P14007
- Ligands
- ZN, SO4
- Pockets
- 18 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-insensitive murein endopeptidase (EC 3.4.99.-) | protein | 232 | 27% helix, 19% strand | P14007 |
| B | Penicillin-insensitive murein endopeptidase (EC 3.4.99.-) | protein | 239 | 28% helix, 18% strand | P14007 |
| C, D, E | Penicillin-insensitive murein endopeptidase (EC 3.4.99.-) | protein | 241 | 27% helix, 18% strand | P14007 |
| F | Penicillin-insensitive murein endopeptidase (EC 3.4.99.-) | protein | 240 | 28% helix, 18% strand | P14007 |
Ligands and binding sites
- ZN · Zinc ion · metal · 9 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 336 | 0.72 | 0.84 | 41 | empty |
| 2 | 531 | 0.71 | 0.80 | 47 | empty |
| 3 | 256 | 0.66 | 0.83 | 30 | empty |
| 4 | 337 | 0.58 | 0.76 | 28 | empty |
| 5 | 53 | 0.53 | 0.89 | 16 | empty |
Interfaces
7 interfaces between chains.
- A–B · 745 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 727 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 443 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 380 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 255 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified, 12 disulfide (engineered, disulfide).
Compared structures
- 1U10 · MEPA, active form with ZN in P1 · the same entry in another collection · chain A against A, 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 P14007
- Elsewhere: RCSB PDB 1U10 · PDBe 1U10 · UniProt P14007
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