MolNFT v1 · #177153 · protein
Crystal structure of kpc-2 in complex with (S)-2-(1-hydroxy-1,3- DIHYDROBENZO[C][1,2]OXABOROL-3-YL)ACRYLIC acid (4A-(S))
7E9A · Beta-lactamase: “Crystal structure of kpc-2 in complex with (S)-2-(1-hydroxy-1,3- DIHYDROBENZO[C][1,2]OXABOROL-3-YL)ACRYLIC…”. X-ray diffraction, 1 ligand (J00), 8 pockets (best druggability 0.75). MolNFT v1 #177153 on GenesisL1: 3D…
- PDB
- 7E9A
- Type
- protein
- Length
- 1,051 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q93LQ9
- Ligands
- J00
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Beta-lactamase (EC 3.5.2.6) | protein | 264 | 42% helix, 17% strand | Q93LQ9 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 261 | 42% helix, 17% strand | Q93LQ9 |
| D | Beta-lactamase (EC 3.5.2.6) | protein | 262 | 43% helix, 17% strand | Q93LQ9 |
Ligands and binding sites
- J00 · 2-[(3S)-1-oxidanyl-3H-2,1-benzoxaborol-3-yl]prop-2-enoic acid · ligand · 4 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 10 copies · chains A, B, C, D
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D
- ACY · Acetic acid · additive · 3 copies · chains A, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 865 | 0.75 | 0.79 | 111 | J00, GOL |
| 2 | 522 | 0.65 | 0.77 | 48 | PEG |
| 3 | 237 | 0.63 | 0.82 | 37 | GOL |
| 4 | 178 | 0.56 | 0.80 | 31 | empty |
| 5 | 66 | 0.31 | 0.74 | 11 | empty |
Interfaces
5 interfaces between chains.
- C–D · 860 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 833 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 415 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 341 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 175 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 disulfide (covalent ligand, disulfide).
Compared structures
- 7E9A · Crystal structure of KPC-2 in complex with (S)-2-(1-hydroxy-1,3-dihydrobenzo[c][1,2]oxabor… · 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 Q93LQ9
- Elsewhere: RCSB PDB 7E9A · PDBe 7E9A · UniProt Q93LQ9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.