Research workbench
Structure of papua new guinea mbl-1(PNGM-1) native
Analyse Structure of papua new guinea mbl-1(PNGM-1) native in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6J4N
- Type
- protein
- Length
- 2,976 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallo-beta-lactamases pngm-1
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Metallo-beta-lactamases pngm-1 | protein | 372 | 30% helix, 24% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 16 copies · chains A, B, C, D, E, F, G, 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 | 821 | 0.84 | 0.86 | 98 | empty |
| 2 | 776 | 0.77 | 0.81 | 61 | empty |
| 3 | 400 | 0.76 | 0.86 | 55 | empty |
| 4 | 778 | 0.76 | 0.80 | 61 | empty |
| 5 | 379 | 0.76 | 0.86 | 49 | empty |
Interfaces
13 interfaces between chains.
- A–F · 4932 Ų buried · 80 hydrogen bonds · protein-protein
- D–G · 4923 Ų buried · 69 hydrogen bonds · protein-protein
- B–E · 4921 Ų buried · 72 hydrogen bonds · protein-protein
- C–H · 4913 Ų buried · 67 hydrogen bonds · protein-protein
- A–D · 1633 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 6J4N · Structure of papua new guinea MBL-1(PNGM-1) native · 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
- Elsewhere: RCSB PDB 6J4N · PDBe 6J4N
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