Research workbench
Crystal structure of zn-dependent arginine carboxypeptidase complexed with zinc
Analyse Crystal structure of zn-dependent arginine carboxypeptidase complexed with zinc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DUG
- Type
- protein
- Length
- 3,154 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zn-dependent arginine carboxypeptidase
- Ligands
- ARG, ZN
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, G, H | Zn-dependent arginine carboxypeptidase | protein | 394 | 34% helix, 23% strand | — |
| C, F | Zn-dependent arginine carboxypeptidase | protein | 395 | 36% helix, 22% strand | — |
Ligands and binding sites
- ARG · Arginine · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- ZN · Zinc ion · metal · 32 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 10 copies · chains A, B, C, D, G, E, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1035 | 0.78 | 0.80 | 74 | ZN, ARG |
| 2 | 798 | 0.78 | 0.82 | 73 | ARG |
| 3 | 820 | 0.78 | 0.82 | 73 | ZN, ARG, GOL |
| 4 | 835 | 0.78 | 0.81 | 69 | ZN, ARG, GOL |
| 5 | 1072 | 0.78 | 0.80 | 77 | ARG |
Interfaces
16 interfaces between chains.
- C–H · 951 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 944 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 941 Ų buried · 14 hydrogen bonds · protein-protein
- D–G · 934 Ų buried · 13 hydrogen bonds · protein-protein
- B–H · 820 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 8 modified (disulfide, carboxylation).
Compared structures
- 3DUG · Crystal structure of zn-dependent arginine carboxypeptidase complexed with zinc · the same entry in another collection · chain B against B, 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
- Elsewhere: RCSB PDB 3DUG · PDBe 3DUG
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