Research workbench
E. COLI microcin-processing metalloprotease TLDD/E with actinonin bound
Analyse E. COLI microcin-processing metalloprotease TLDD/E with actinonin bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NJB
- Type
- protein
- Length
- 1,849 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metalloprotease tldd; Metalloprotease pmba
- EC
- 3.4.-.-
- UniProt
- P0AGG8, P0AFK0
- Ligands
- BB2, ZN
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metalloprotease tldd (EC 3.4.-.-) | protein | 480 | 24% helix, 42% strand | P0AGG8 |
| B, D | Metalloprotease pmba (EC 3.4.-.-) | protein | 445 | 26% helix, 37% strand | P0AFK0 |
| C | Metalloprotease tldd (EC 3.4.-.-) | protein | 479 | 24% helix, 42% strand | P0AGG8 |
Ligands and binding sites
- BB2 · Actinonin · ligand · 2 copies · chains A, C
- ZN · Zinc ion · metal · 2 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, C, D
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 862 | 0.74 | 0.78 | 91 | ZN, BB2 |
| 2 | 500 | 0.70 | 0.80 | 61 | empty |
| 3 | 517 | 0.70 | 0.80 | 63 | ZN, BB2 |
| 4 | 671 | 0.69 | 0.77 | 79 | empty |
| 5 | 336 | 0.66 | 0.81 | 55 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2790 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 2773 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 344 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5NJB · E. coli Microcin-processing metalloprotease TldD/E with actinonin bound · the same entry in another collection · chain A against A, TM-score 1.00
- P0AGG8 · AlphaFold monomer V2.0 prediction for metalloprotease tldd (P0AGG8) · a predicted model of the same protein · chain C against A, TM-score 1.00
- P0AFK0 · AlphaFold monomer V2.0 prediction for metalloprotease pmba (P0AFK0) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P0AGG8
- Every structure of UniProt P0AFK0
- Elsewhere: RCSB PDB 5NJB · PDBe 5NJB · UniProt P0AGG8 · UniProt P0AFK0
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