MolNFT v1 · #174553 · protein
The mutant variant of pngm-1. H257 was substituted for alanine to study substrate binding.
7BZ3 · Metallo-beta-lactamase pngm-1: “The mutant variant of pngm-1. H257 was substituted for alanine to study substrate binding.”. X-ray diffraction, 1 ligand (ZN), 10 pockets (best druggability 0.83). MolNFT v1 #174553 on GenesisL1: 3D…
- PDB
- 7BZ3
- Type
- protein
- Length
- 1,347 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallo-beta-lactamase pngm-1
- EC
- 3.5.2.6
- UniProt
- A0A2U8UYM6
- Ligands
- ZN
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Metallo-beta-lactamase pngm-1 (EC 3.5.2.6) | protein | 344 | 28% helix, 26% strand | A0A2U8UYM6 |
| C | Metallo-beta-lactamase pngm-1 (EC 3.5.2.6) | protein | 335 | 25% helix, 27% strand | A0A2U8UYM6 |
| D | Metallo-beta-lactamase pngm-1 (EC 3.5.2.6) | protein | 324 | 27% helix, 27% strand | A0A2U8UYM6 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1108 | 0.83 | 0.84 | 148 | empty |
| 2 | 761 | 0.77 | 0.81 | 57 | empty |
| 3 | 555 | 0.74 | 0.81 | 41 | empty |
| 4 | 301 | 0.62 | 0.79 | 43 | empty |
| 5 | 328 | 0.60 | 0.77 | 43 | empty |
Interfaces
6 interfaces between chains.
- A–C · 4186 Ų buried · 54 hydrogen bonds · protein-protein
- B–D · 4163 Ų buried · 57 hydrogen bonds · protein-protein
- C–D · 631 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 588 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 566 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7BZ3 · The mutant variant of PNGM-1. H257 was substituted for alanine to study substrate binding. · 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 A0A2U8UYM6
- Elsewhere: RCSB PDB 7BZ3 · PDBe 7BZ3 · UniProt A0A2U8UYM6
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