MolNFT v1 · #86446 · protein
Crystal structure of metallo-carboxypeptidase from burkholderia cenocepacia
4B6Z · Family M14 unassigned peptidase: “Crystal structure of metallo-carboxypeptidase from burkholderia cenocepacia”. X-ray diffraction, 2 ligands (ZN, CL), 16 pockets (best druggability 0.77). MolNFT v1 #86446 on GenesisL1: 3D structure…
- PDB
- 4B6Z
- Type
- protein
- Length
- 1,518 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Family M14 unassigned peptidase
- UniProt
- B4EEQ5
- Ligands
- ZN, CL
- Pockets
- 16 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Family M14 unassigned peptidase | protein | 380 | 31% helix, 23% strand | B4EEQ5 |
| B | Family M14 unassigned peptidase | protein | 382 | 31% helix, 24% strand | B4EEQ5 |
| C | Family M14 unassigned peptidase | protein | 376 | 31% helix, 25% strand | B4EEQ5 |
| D | Family M14 unassigned peptidase | protein | 380 | 31% helix, 24% strand | B4EEQ5 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 3 copies · chains B, C, D
- GOL · Glycerol · additive · 9 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 7 copies · chains B, C, D
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.77 | 0.99 | 30 | empty |
| 2 | 95 | 0.75 | 0.96 | 32 | empty |
| 3 | 71 | 0.72 | 0.97 | 26 | empty |
| 4 | 78 | 0.71 | 0.96 | 26 | PEG |
| 5 | 333 | 0.60 | 0.78 | 43 | EDO |
Interfaces
5 interfaces between chains.
- C–D · 1509 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1466 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 170 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 153 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 121 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4B6Z · Crystal structure of metallo-carboxypeptidase from Burkholderia cenocepacia · the same entry in another collection · 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 B4EEQ5
- Elsewhere: RCSB PDB 4B6Z · PDBe 4B6Z · UniProt B4EEQ5
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