Research workbench
Seleno-methionine pngm-1 from deep-sea sediment metagenome
Analyse Seleno-methionine pngm-1 from deep-sea sediment metagenome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JKW
- 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 0.82
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Metallo-beta-lactamases pngm-1 | protein | 372 | 29% helix, 23% 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 552 | 0.82 | 0.88 | 89 | empty |
| 2 | 747 | 0.78 | 0.82 | 58 | empty |
| 3 | 428 | 0.77 | 0.86 | 56 | empty |
| 4 | 413 | 0.77 | 0.86 | 57 | empty |
| 5 | 412 | 0.77 | 0.86 | 55 | empty |
Interfaces
13 interfaces between chains.
- A–F · 4967 Ų buried · 73 hydrogen bonds · protein-protein
- C–H · 4967 Ų buried · 68 hydrogen bonds · protein-protein
- B–E · 4961 Ų buried · 73 hydrogen bonds · protein-protein
- D–G · 4945 Ų buried · 68 hydrogen bonds · protein-protein
- A–D · 1651 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 136 modified (engineered).
Compared structures
- 6JKW · Seleno-methionine PNGM-1 from deep-sea sediment metagenome · 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 6JKW · PDBe 6JKW
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