Research workbench
Crystal structure of the metallo-beta-lactamase blab of chryseobacterium meningosepticum in complex with the inhibitor D- captopril
Analyse Crystal structure of the metallo-beta-lactamase blab of chryseobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1M2X
- Type
- protein
- Length
- 874 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Class B carbapenemase blab-1
- EC
- 3.5.2.6
- UniProt
- O08498
- Ligands
- MCO, ZN, NA
- Pockets
- 8 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Class B carbapenemase blab-1 (EC 3.5.2.6) | protein | 219 | 26% helix, 33% strand | O08498 |
| C | Class B carbapenemase blab-1 (EC 3.5.2.6) | protein | 217 | 28% helix, 33% strand | O08498 |
Ligands and binding sites
- MCO · 1-(3-mercapto-2-methyl-propionyl)-pyrrolidine-2-carboxylic acid · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 12 copies · chains A, B, C, D
- NA · Sodium ion · metal · chains A
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 246 | 0.63 | 0.82 | 27 | empty |
| 2 | 264 | 0.63 | 0.81 | 26 | empty |
| 3 | 227 | 0.60 | 0.80 | 24 | empty |
| 4 | 406 | 0.59 | 0.76 | 46 | MCO |
| 5 | 218 | 0.59 | 0.81 | 28 | empty |
Interfaces
2 interfaces between chains.
- A–B · 536 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 535 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1M2X · Crystal Structure of the metallo-beta-lactamase BlaB of Chryseobacterium meningosepticum… · the same entry in another collection · chain D against D, TM-score 1.00
- O08498 · AlphaFold monomer V2.0 prediction for metallo-beta-lactamase type 2 (O08498) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 O08498
- Elsewhere: RCSB PDB 1M2X · PDBe 1M2X · UniProt O08498
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