Research workbench
Crystal structure of oxa-10LOOP48 in complex with hydrolyzed doripenem
Analyse Crystal structure of oxa-10LOOP48 in complex with hydrolyzed doripenem in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZRG
- Type
- protein
- Length
- 484 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q7BNC2
- Ligands
- QP2, SO4, CL
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase (EC 3.5.2.6) | protein | 242 | 40% helix, 22% strand | Q7BNC2 |
Ligands and binding sites
- QP2 · (2~{S},3~{R})-4-[(3~{S},5~{S})-5-[[[azanyl-bis(oxidanyl)methyl]amino]methyl]pyrrolidin-3-yl]sulfanyl-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-3-methyl-2,3-dihydro-1~{H}-pyrrole-5-carboxylic acid · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.74 | 0.93 | 30 | empty |
| 2 | 179 | 0.71 | 0.89 | 36 | EDO |
| 3 | 245 | 0.52 | 0.75 | 39 | empty |
| 4 | 107 | 0.42 | 0.77 | 22 | EDO |
| 5 | 59 | 0.33 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1321 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 modified (disulfide, carboxylation).
Compared structures
- 6ZRG · Crystal structure of OXA-10loop48 in complex with hydrolyzed doripenem · 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 Q7BNC2
- Elsewhere: RCSB PDB 6ZRG · PDBe 6ZRG · UniProt Q7BNC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.