MolNFT v1 · #174568 · protein
The mutant variant of pngm-1. H91 was substituted for alanine to study metal coordination.
7BZI · Metallo-beta-lactamase pngm-1: “The mutant variant of pngm-1. H91 was substituted for alanine to study metal coordination.”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.83). MolNFT v1 #174568 on GenesisL1: 3D…
- PDB
- 7BZI
- Type
- protein
- Length
- 2,887 residues
- Chains
- 8
- 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
- 20 · best druggability 0.83
Structure
x-ray diffraction · 7 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Metallo-beta-lactamase pngm-1 (EC 3.5.2.6) | protein | 366 | 30% helix, 23% strand | A0A2U8UYM6 |
| B | Metallo-beta-lactamase pngm-1 (EC 3.5.2.6) | protein | 365 | 30% helix, 24% strand | A0A2U8UYM6 |
| C, H | Metallo-beta-lactamase pngm-1 (EC 3.5.2.6) | protein | 357 | 30% helix, 25% strand | A0A2U8UYM6 |
| F | Metallo-beta-lactamase pngm-1 (EC 3.5.2.6) | protein | 363 | 29% helix, 25% strand | A0A2U8UYM6 |
| E | Metallo-beta-lactamase pngm-1 (EC 3.5.2.6) | protein | 359 | 29% helix, 24% strand | A0A2U8UYM6 |
| D | Metallo-beta-lactamase pngm-1 (EC 3.5.2.6) | protein | 360 | 29% helix, 24% strand | A0A2U8UYM6 |
| A | Metallo-beta-lactamase pngm-1 (EC 3.5.2.6) | protein | 360 | 31% helix, 24% strand | A0A2U8UYM6 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains G, B, C, F, E, D, A, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 813 | 0.83 | 0.86 | 99 | empty |
| 2 | 525 | 0.81 | 0.88 | 86 | empty |
| 3 | 543 | 0.81 | 0.87 | 92 | empty |
| 4 | 518 | 0.76 | 0.83 | 52 | empty |
| 5 | 507 | 0.74 | 0.82 | 49 | empty |
Interfaces
13 interfaces between chains.
- G–H · 4979 Ų buried · 72 hydrogen bonds · protein-protein
- C–D · 4931 Ų buried · 74 hydrogen bonds · protein-protein
- F–E · 4917 Ų buried · 75 hydrogen bonds · protein-protein
- B–A · 4913 Ų buried · 71 hydrogen bonds · protein-protein
- F–H · 1284 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 7BZI · The mutant variant of PNGM-1. H91 was substituted for alanine to study metal coordination. · the same entry in another collection · chain G against G, 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 7BZI · PDBe 7BZI · UniProt A0A2U8UYM6
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