Research workbench
Crystal structure of 5-{[AMINO(IMINO)METHYL]AMINO}-2- (SULFANYLMETHYL)PENTANOIC acid bound to activated porcine pancreatic carboxypeptidase B
Analyse Crystal structure of 5-{[AMINO(IMINO)METHYL]AMINO}-2- (SULFANYLMETHYL)PENTANOIC… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZG9
- Type
- protein
- Length
- 914 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Procarboxypeptidase B
- EC
- 3.4.17.2
- UniProt
- P09955
- Ligands
- L06, ZN
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Procarboxypeptidase B (EC 3.4.17.2) | protein | 305 | 38% helix, 17% strand | P09955 |
| C | Procarboxypeptidase B (EC 3.4.17.2) | protein | 304 | 37% helix, 17% strand | P09955 |
Ligands and binding sites
- L06 · 5-{[amino(imino)methyl]amino}-2-(sulfanylmethyl)pentanoic acid · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 105 | 0.65 | 0.90 | 23 | L06 |
| 2 | 84 | 0.62 | 0.90 | 20 | L06 |
| 3 | 102 | 0.61 | 0.88 | 22 | L06 |
| 4 | 369 | 0.57 | 0.75 | 39 | empty |
| 5 | 52 | 0.28 | 0.75 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–B · 453 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 140 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 1ZG9 · Crystal Structure of 5-{[amino(imino)methyl]amino}-2-(sulfanylmethyl)pentanoic acid Bound… · the same entry in another collection · chain A against A, TM-score 1.00
- P09955 · AlphaFold monomer V2.0 prediction for carboxypeptidase B (P09955) · a predicted model of the same protein · 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 P09955
- Elsewhere: RCSB PDB 1ZG9 · PDBe 1ZG9 · UniProt P09955
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