MolNFT v1 · #83514 · protein
The periplasmic PDZ tandem fragment of the rsep homologue from aquifex aeolicus in complex with the Fab fragment
3WKM · Putative zinc metalloprotease AQ_1964: “The periplasmic PDZ tandem fragment of the rsep homologue from aquifex aeolicus in complex with the Fab…”. X-ray diffraction, 13 pockets (best druggability 0.80). MolNFT v1 #83514 on…
- 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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