MolNFT v1 · #118228 · protein
Crystal structure of beta-LACTAMASE/D-alanine carboxypeptidase from pseudomonas syringae
5EVI: “Crystal structure of beta-LACTAMASE/D-alanine carboxypeptidase from pseudomonas syringae”. X-ray diffraction, 1 ligand (SO4), 17 pockets (best druggability 0.67). MolNFT v1 #118228 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5EVI
- Type
- protein
- Length
- 1,430 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-LACTAMASE/D-alanine carboxypeptidase
- EC
- 3.5.2.6
- UniProt
- Q87Z37
- Ligands
- SO4
- Pockets
- 17 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Beta-LACTAMASE/D-alanine carboxypeptidase (EC 3.5.2.6) | protein | 356 | 40% helix, 21% strand | Q87Z37 |
| B, D | Beta-LACTAMASE/D-alanine carboxypeptidase (EC 3.5.2.6) | protein | 359 | 40% helix, 22% strand | Q87Z37 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.67 | 0.96 | 14 | empty |
| 2 | 406 | 0.66 | 0.79 | 35 | empty |
| 3 | 382 | 0.66 | 0.80 | 40 | EDO |
| 4 | 237 | 0.57 | 0.78 | 21 | empty |
| 5 | 196 | 0.56 | 0.80 | 28 | SO4 |
Interfaces
4 interfaces between chains.
- A–D · 708 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 520 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 506 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 33 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 57 modified (engineered, methylation).
Compared structures
- 5EVI · Crystal Structure of Beta-Lactamase/D-Alanine Carboxypeptidase from Pseudomonas syringae · 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 Q87Z37
- Elsewhere: RCSB PDB 5EVI · PDBe 5EVI · UniProt Q87Z37
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