Research workbench
Carboxypeptidase G2 modified with a versatile bioconjugate for metalloprotein design
Analyse Carboxypeptidase G2 modified with a versatile bioconjugate for metalloprotein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XJ5
- Type
- protein
- Length
- 3,107 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxypeptidase G2
- EC
- 3.4.17.11
- UniProt
- P06621
- Ligands
- ZN, SO4
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Carboxypeptidase G2 (EC 3.4.17.11) | protein | 389 | 37% helix, 25% strand | P06621 |
| B, H | Carboxypeptidase G2 (EC 3.4.17.11) | protein | 389 | 38% helix, 26% strand | P06621 |
| D | Carboxypeptidase G2 (EC 3.4.17.11) | protein | 386 | 37% helix, 26% strand | P06621 |
| F | Carboxypeptidase G2 (EC 3.4.17.11) | protein | 389 | 37% helix, 26% strand | P06621 |
| G | Carboxypeptidase G2 (EC 3.4.17.11) | protein | 387 | 37% helix, 26% strand | P06621 |
Ligands and binding sites
- ZN · Zinc ion · metal · 56 copies · chains A, E, B, C, D, G, F, H
- SO4 · Sulfate ion · ion · 2 copies · chains C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 953 | 0.76 | 0.79 | 95 | SO4, ZN |
| 2 | 86 | 0.75 | 0.97 | 35 | empty |
| 3 | 962 | 0.75 | 0.78 | 78 | empty |
| 4 | 864 | 0.72 | 0.77 | 83 | empty |
| 5 | 62 | 0.72 | 0.97 | 22 | empty |
Interfaces
12 interfaces between chains.
- E–H · 1278 Ų buried · 12 hydrogen bonds · protein-protein
- F–G · 1164 Ų buried · 10 hydrogen bonds · protein-protein
- F–H · 469 Ų buried · 4 hydrogen bonds · protein-protein
- E–G · 457 Ų buried · 4 hydrogen bonds · protein-protein
- C–E · 347 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 6XJ5 · Carboxypeptidase G2 modified with a versatile bioconjugate for metalloprotein design · the same entry in another collection · chain H against H, TM-score 1.00
- P06621 · AlphaFold monomer V2.0 prediction for carboxypeptidase G2 (P06621) · a predicted model of the same protein · chain E against A, TM-score 0.99
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 6XJ5 · PDBe 6XJ5 · UniProt P06621
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