MolNFT v1 · #156844 · protein
Crystal structure of the new deli metallo beta lactamase variant 4 from klebsiella pneumoniae
6MGZ · Ndm-4: “Crystal structure of the new deli metallo beta lactamase variant 4 from klebsiella pneumoniae”. X-ray diffraction, 2 ligands (ZN, MG), 4 pockets (best druggability 0.77). MolNFT v1 #156844 on GenesisL1: 3D structure, binding…
- PDB
- 6MGZ
- Type
- protein
- Length
- 458 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ndm-4
- UniProt
- A0A0G2ST15
- Ligands
- ZN, MG
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ndm-4 | protein | 230 | 26% helix, 32% strand | A0A0G2ST15 |
| B | Ndm-4 | protein | 228 | 25% helix, 32% strand | A0A0G2ST15 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B
- MG · Magnesium ion · metal · chains B
- FMT · Formic acid · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 103 | 0.77 | 0.97 | 21 | empty |
| 2 | 103 | 0.55 | 0.85 | 31 | empty |
| 3 | 63 | 0.28 | 0.73 | 18 | ZN, FMT |
| 4 | 68 | 0.28 | 0.73 | 23 | ZN, FMT |
Interfaces
1 interface between chains.
- A–B · 868 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6MGZ · Crystal Structure of the New Deli Metallo Beta Lactamase Variant 4 from Klebsiella… · 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 A0A0G2ST15
- Elsewhere: RCSB PDB 6MGZ · PDBe 6MGZ · UniProt A0A0G2ST15
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.