Research workbench
Crystal structure of a circular permutation and computationally designed pro-enzyme of carboxypeptidase G2
Analyse Crystal structure of a circular permutation and computationally designed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7M6U
- Type
- protein
- Length
- 1,528 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxypeptidase G2 circular permuation pro-domain fusion
- EC
- 3.4.17.11
- UniProt
- P06621
- Ligands
- ZN, SO4
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carboxypeptidase G2 circular permuation pro-domain fusion (EC 3.4.17.11) | protein | 391 | 38% helix, 26% strand | P06621 |
| B | Carboxypeptidase G2 circular permuation pro-domain fusion (EC 3.4.17.11) | protein | 392 | 37% helix, 27% strand | P06621 |
| C | Carboxypeptidase G2 circular permuation pro-domain fusion (EC 3.4.17.11) | protein | 389 | 38% helix, 26% strand | P06621 |
| D | Carboxypeptidase G2 circular permuation pro-domain fusion (EC 3.4.17.11) | protein | 356 | 34% helix, 23% strand | P06621 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 823 | 0.76 | 0.80 | 88 | empty |
| 2 | 1069 | 0.76 | 0.78 | 90 | empty |
| 3 | 402 | 0.72 | 0.83 | 49 | empty |
| 4 | 246 | 0.56 | 0.78 | 32 | empty |
| 5 | 234 | 0.54 | 0.78 | 34 | empty |
Interfaces
4 interfaces between chains.
- A–B · 417 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 118 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 86 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 40 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7M6U · Crystal structure of a circular permutation and computationally designed pro-enzyme of… · the same entry in another collection · chain D against D, TM-score 1.00
- P06621 · AlphaFold monomer V2.0 prediction for carboxypeptidase G2 (P06621) · a predicted model of the same protein · chain A against A, TM-score 0.83
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 P06621
- Elsewhere: RCSB PDB 7M6U · PDBe 7M6U · UniProt P06621
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