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The periplasmic PDZ tandem fragment of the rsep homologue from aquifex aeolicus in complex with the Fab fragment
Analyse The periplasmic PDZ tandem fragment of the rsep homologue from aquifex aeolicus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WKM
- Type
- protein
- Length
- 1,194 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative zinc metalloprotease AQ_1964; Mouse IGG1-kappa Fab (heavy chain); Mouse…
- EC
- 3.4.24.-
- UniProt
- O67776
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 10% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative zinc metalloprotease AQ_1964 (EC 3.4.24.-) | protein | 176 | 21% helix, 36% strand | O67776 |
| H | Mouse IGG1-kappa Fab (heavy chain) | protein | 216 | 6% helix, 55% strand | — |
| L | Mouse IGG1-kappa Fab (light chain) | protein | 215 | 6% helix, 53% strand | — |
| B | Putative zinc metalloprotease AQ_1964 (EC 3.4.24.-) | protein | 179 | 21% helix, 36% strand | O67776 |
| I | Mouse IGG1-kappa Fab (heavy chain) | protein | 194 | 3% helix, 52% strand | — |
| M | Mouse IGG1-kappa Fab (light chain) | protein | 214 | 6% helix, 51% strand | — |
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1063 | 0.80 | 0.81 | 93 | empty |
| 2 | 757 | 0.80 | 0.83 | 70 | empty |
| 3 | 50 | 0.69 | 0.97 | 17 | empty |
| 4 | 739 | 0.66 | 0.74 | 67 | empty |
| 5 | 593 | 0.63 | 0.75 | 65 | empty |
Interfaces
7 interfaces between chains.
- H–L · 1980 Ų buried · 28 hydrogen bonds · protein-protein
- I–M · 1924 Ų buried · 27 hydrogen bonds · protein-protein
- B–I · 841 Ų buried · 13 hydrogen bonds · protein-protein
- A–H · 808 Ų buried · 10 hydrogen bonds · protein-protein
- B–M · 695 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3WKM · The periplasmic PDZ tandem fragment of the RseP homologue from Aquifex aeolicus in… · the same entry in another collection · chain I against I, TM-score 1.00
- O67776 · AlphaFold monomer V2.0 prediction for putative zinc metalloprotease AQ_1964 (O67776) · a predicted model of the same protein · chain B against A, TM-score 0.87
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 O67776
- Elsewhere: RCSB PDB 3WKM · PDBe 3WKM · UniProt O67776
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