Research workbench
The mutant variant of pngm-1. H279A was substituted for alanine to study metal coordination.
Analyse The mutant variant of pngm-1. H279A was substituted for alanine to study metal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BYQ
- Type
- protein
- Length
- 1,444 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
- 16 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metallo-beta-lactamase pngm-1 (EC 3.5.2.6) | protein | 362 | 31% helix, 25% strand | A0A2U8UYM6 |
| B, C | Metallo-beta-lactamase pngm-1 (EC 3.5.2.6) | protein | 360 | 27% helix, 24% strand | A0A2U8UYM6 |
| D | Metallo-beta-lactamase pngm-1 (EC 3.5.2.6) | protein | 362 | 26% helix, 25% strand | A0A2U8UYM6 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 380 | 0.76 | 0.86 | 51 | empty |
| 2 | 490 | 0.74 | 0.83 | 45 | ZN |
| 3 | 343 | 0.74 | 0.86 | 51 | empty |
| 4 | 448 | 0.73 | 0.82 | 41 | empty |
| 5 | 120 | 0.72 | 0.93 | 39 | empty |
Interfaces
6 interfaces between chains.
- A–D · 5010 Ų buried · 77 hydrogen bonds · protein-protein
- B–C · 4940 Ų buried · 71 hydrogen bonds · protein-protein
- C–D · 1581 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1551 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 765 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7BYQ · The mutant variant of PNGM-1. H279A was substituted for alanine to study metal… · 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 7BYQ · PDBe 7BYQ · UniProt A0A2U8UYM6
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