MolNFT v1 · #84095 · protein
Crystal structure of metallo-beta-lactamase H48A from thermotoga maritima
3X2X · UPF0173 metal-dependent hydrolase TM_1162: “Crystal structure of metallo-beta-lactamase H48A from thermotoga maritima”. X-ray diffraction, 1 ligand (MN), 8 pockets (best druggability 0.83). MolNFT v1 #84095 on GenesisL1: 3D…
- PDB
- 3X2X
- Type
- protein
- Length
- 681 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UPF0173 metal-dependent hydrolase TM_1162
- UniProt
- Q9X0P5
- Ligands
- MN
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | UPF0173 metal-dependent hydrolase TM_1162 | protein | 227 | 23% helix, 30% strand | Q9X0P5 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 176 | 0.83 | 0.97 | 27 | empty |
| 2 | 133 | 0.44 | 0.76 | 33 | empty |
| 3 | 50 | 0.35 | 0.79 | 11 | MN |
| 4 | 52 | 0.35 | 0.78 | 10 | MN |
| 5 | 50 | 0.34 | 0.78 | 10 | MN |
Interfaces
3 interfaces between chains.
- A–B · 1092 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1083 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1079 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3X2X · Crystal structure of metallo-beta-lactamase H48A from Thermotoga maritima · the same entry in another collection · chain A against A, TM-score 1.00
- Q9X0P5 · AlphaFold monomer V2.0 prediction for UPF0173 metal-dependent hydrolase TM_1162 (Q9X0P5) · a predicted model of the same protein · chain A 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 Q9X0P5
- Elsewhere: RCSB PDB 3X2X · PDBe 3X2X · UniProt Q9X0P5
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