Research workbench
E. COLI microcin-processing metalloprotease TLDD/E (tldd E263A mutant) with hexapeptide bound
Analyse E. COLI microcin-processing metalloprotease TLDD/E (tldd E263A mutant) with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NJC
- Type
- protein
- Length
- 1,856 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metalloprotease tldd; Metalloprotease pmba; Val-leu-glu-asp-arg-ile
- EC
- 3.4.-.-
- UniProt
- P0AGG8, P0AFK0
- Ligands
- NA, ZN
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 25% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metalloprotease tldd (EC 3.4.-.-) | protein | 479 | 25% helix, 42% strand | P0AGG8 |
| B | Metalloprotease pmba (EC 3.4.-.-) | protein | 443 | 26% helix, 37% strand | P0AFK0 |
| C | Metalloprotease tldd (EC 3.4.-.-) | protein | 480 | 25% helix, 42% strand | P0AGG8 |
| D | Metalloprotease pmba (EC 3.4.-.-) | protein | 442 | 25% helix, 38% strand | P0AFK0 |
| E, F | Val-leu-glu-asp-arg-ile | protein | 6 | 0% helix, 67% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 2 copies · chains A, E, C, F
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B, D, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 844 | 0.75 | 0.79 | 81 | empty |
| 2 | 757 | 0.73 | 0.78 | 70 | empty |
| 3 | 780 | 0.73 | 0.78 | 87 | empty |
| 4 | 669 | 0.72 | 0.79 | 77 | empty |
| 5 | 642 | 0.71 | 0.78 | 82 | EDO |
Interfaces
6 interfaces between chains.
- C–D · 2782 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 2769 Ų buried · 39 hydrogen bonds · protein-protein
- C–F · 563 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 504 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 317 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5NJC · E. coli Microcin-processing metalloprotease TldD/E (TldD E263A mutant) with hexapeptide… · the same entry in another collection · chain F against F, 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 D 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 5NJC · PDBe 5NJC · UniProt P0AGG8 · UniProt P0AFK0
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