Research workbench
Crystal structure of zn-dependent arginine carboxypeptidase
Analyse Crystal structure of zn-dependent arginine carboxypeptidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BE7
- Type
- protein
- Length
- 3,160 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zn-dependent arginine carboxypeptidase
- Ligands
- ARG, MG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Zn-dependent arginine carboxypeptidase | protein | 398 | 33% helix, 23% strand | — |
| B, D, F, H | Zn-dependent arginine carboxypeptidase | protein | 395 | 34% helix, 21% strand | — |
| C, E, G | Zn-dependent arginine carboxypeptidase | protein | 394 | 34% helix, 23% strand | — |
Ligands and binding sites
- ARG · Arginine · ligand · 8 copies · chains E, B, D, C, F, G, H, A
- MG · Magnesium ion · metal · 2 copies · chains F, H
- GOL · Glycerol · additive · 16 copies · chains A, B, C, D, F, H, G, 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1087 | 0.78 | 0.80 | 75 | ARG, GOL |
| 2 | 1072 | 0.78 | 0.80 | 73 | ARG |
| 3 | 1009 | 0.77 | 0.79 | 78 | ARG |
| 4 | 1102 | 0.77 | 0.79 | 82 | ARG, GOL |
| 5 | 1110 | 0.77 | 0.79 | 77 | ARG |
Interfaces
16 interfaces between chains.
- D–G · 966 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 963 Ų buried · 13 hydrogen bonds · protein-protein
- C–H · 953 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 948 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 822 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3BE7 · Crystal structure of Zn-dependent arginine carboxypeptidase · 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 3BE7 · PDBe 3BE7
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