Research workbench
Structure of a PDZ-protease bound to a substrate-binding adaptor
Analyse Structure of a PDZ-protease bound to a substrate-binding adaptor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WQL
- Type
- protein
- Length
- 1,853 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipoprotein nlpi; Tail-specific protease; Ala-ala-ala-ala-ala-ala; Ala-ala-ala-ala…
- EC
- 3.4.21.102
- UniProt
- P0AFB1, P23865
- Pockets
- 20 · best druggability 0.61
Structure
x-ray diffraction · 7 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Lipoprotein nlpi | protein | 268 | 75% helix, 0% strand | P0AFB1 |
| A | Lipoprotein nlpi | protein | 270 | 74% helix, 0% strand | P0AFB1 |
| C | Tail-specific protease (EC 3.4.21.102) | protein | 648 | 43% helix, 17% strand | P23865 |
| D | Tail-specific protease (EC 3.4.21.102) | protein | 647 | 42% helix, 17% strand | P23865 |
| F, H | Ala-ala-ala-ala-ala-ala | protein | 6 | 0% helix, 67% strand | — |
| E | Ala-ala-ala-ala | protein | 4 | 0% helix, 50% strand | — |
| G | Leu-ser-arg-ser | protein | 4 | 0% helix, 50% strand | — |
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 329 | 0.61 | 0.78 | 43 | empty |
| 2 | 164 | 0.60 | 0.83 | 30 | empty |
| 3 | 362 | 0.59 | 0.77 | 52 | empty |
| 4 | 228 | 0.53 | 0.77 | 29 | empty |
| 5 | 208 | 0.52 | 0.77 | 35 | empty |
Interfaces
7 interfaces between chains.
- B–A · 1939 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 959 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 829 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 432 Ų buried · 12 hydrogen bonds · protein-protein
- C–G · 425 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5WQL · Structure of a PDZ-protease bound to a substrate-binding adaptor · the same entry in another collection · chain G against G, TM-score 1.00
- P0AFB1 · AlphaFold monomer V2.0 prediction for lipoprotein nlpi (P0AFB1) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P23865 · AlphaFold monomer V2.0 prediction for tail-specific protease (P23865) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P0AFB1
- Every structure of UniProt P23865
- Elsewhere: RCSB PDB 5WQL · PDBe 5WQL · UniProt P0AFB1 · UniProt P23865
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