Research workbench
Serine beta-lactamase-like protein lactb in complex with inhibitor
Analyse Serine beta-lactamase-like protein lactb in complex with inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7V1Y
- Type
- protein
- Length
- 1,588 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine beta-lactamase-like protein lactb, mitochondrial; Ala-ala-B3S
- EC
- 3.4.-.-
- UniProt
- P83111
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 2 distinct chains · 34% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, B, D | Serine beta-lactamase-like protein lactb, mitochondrial (EC 3.4.-.-) | protein | 394 | 34% helix, 18% strand | P83111 |
| E, F, G, H | Ala-ala-B3S | protein | 3 | 0% helix, 0% strand | — |
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 501 | 0.78 | 0.86 | 54 | empty |
| 2 | 473 | 0.78 | 0.86 | 51 | empty |
| 3 | 651 | 0.63 | 0.74 | 54 | empty |
| 4 | 622 | 0.62 | 0.74 | 54 | empty |
| 5 | 183 | 0.60 | 0.82 | 23 | empty |
Interfaces
9 interfaces between chains.
- C–B · 1056 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1054 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 855 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 597 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 595 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 7V1Y · Serine beta-lactamase-like protein LACTB in complex with inhibitor · the same entry in another collection · chain D against D, TM-score 1.00
- P83111 · AlphaFold monomer V2.0 prediction for serine beta-lactamase-like protein lactb… · a predicted model of the same protein · chain A 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 P83111
- Elsewhere: RCSB PDB 7V1Y · PDBe 7V1Y · UniProt P83111
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