MolNFT v1 · #186670 · protein
Crystal structure of K83A mutant of class D beta-lactamase from clostridium difficile 630
7RLR: “Crystal structure of K83A mutant of class D beta-lactamase from clostridium difficile 630”. X-ray diffraction, 2 ligands (NA, CL), 8 pockets (best druggability 0.79). MolNFT v1 #186670 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7RLR
- Type
- protein
- Length
- 1,006 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q188Q3
- Ligands
- NA, CL
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 249 | 37% helix, 20% strand | Q188Q3 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 248 | 37% helix, 19% strand | Q188Q3 |
| C | Beta-lactamase (EC 3.5.2.6) | protein | 255 | 35% helix, 19% strand | Q188Q3 |
| D | Beta-lactamase (EC 3.5.2.6) | protein | 254 | 37% helix, 19% strand | Q188Q3 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains D, B
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 938 | 0.79 | 0.82 | 81 | empty |
| 2 | 451 | 0.62 | 0.76 | 45 | NA |
| 3 | 170 | 0.58 | 0.82 | 22 | empty |
| 4 | 226 | 0.51 | 0.76 | 34 | empty |
| 5 | 216 | 0.50 | 0.75 | 35 | empty |
Interfaces
5 interfaces between chains.
- A–B · 471 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 272 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 209 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 137 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 106 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7RLR · Crystal Structure of K83A Mutant of Class D beta-lactamase from Clostridium difficile 630 · 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 Q188Q3
- Elsewhere: RCSB PDB 7RLR · PDBe 7RLR · UniProt Q188Q3
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