MolNFT v1 · #124798 · protein
Crystal structure of TEM1 beta-lactamase mutant I263L in the presence of 1.2 mpa xenon
5KPU · Beta-lactamase tem: “Crystal structure of TEM1 beta-lactamase mutant I263L in the presence of 1.2 mpa xenon”. X-ray diffraction, 1 ligand (XE), 7 pockets (best druggability 0.76). MolNFT v1 #124798 on GenesisL1: 3D structure…
- PDB
- 5KPU
- Type
- protein
- Length
- 1,052 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase tem
- EC
- 3.5.2.6
- UniProt
- P62593
- Ligands
- XE
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-lactamase tem (EC 3.5.2.6) | protein | 263 | 44% helix, 17% strand | P62593 |
Ligands and binding sites
- XE · Xenon · ion · 13 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1053 | 0.76 | 0.78 | 100 | empty |
| 2 | 892 | 0.75 | 0.79 | 82 | empty |
| 3 | 253 | 0.58 | 0.79 | 36 | empty |
| 4 | 301 | 0.55 | 0.76 | 35 | empty |
| 5 | 115 | 0.43 | 0.77 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–B · 686 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 495 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 282 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 260 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 162 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5KPU · Crystal structure of TEM1 beta-lactamase mutant I263L in the presence of 1.2 MPa xenon · the same entry in another collection · chain D against D, TM-score 1.00
- P62593 · AlphaFold monomer V2.0 prediction for beta-lactamase tem (P62593) · a predicted model of the same protein · chain D 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 P62593
- Elsewhere: RCSB PDB 5KPU · PDBe 5KPU · UniProt P62593
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