MolNFT v1 · #117351 · protein
Crystal structure of mycobacterium tuberculosis L,D-transpeptidase 1 at 1.89 ångström
5E5L: “Crystal structure of mycobacterium tuberculosis L,D-transpeptidase 1 at 1.89 ångström”. X-ray diffraction, 8 pockets (best druggability 0.83). MolNFT v1 #117351 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5E5L
- Type
- protein
- Length
- 772 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L,D-transpeptidase 1
- EC
- 2.3.2.-
- UniProt
- O53638
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L,D-transpeptidase 1 (EC 2.3.2.-) | protein | 190 | 11% helix, 46% strand | O53638 |
| B | L,D-transpeptidase 1 (EC 2.3.2.-) | protein | 200 | 10% helix, 44% strand | O53638 |
| C | L,D-transpeptidase 1 (EC 2.3.2.-) | protein | 190 | 9% helix, 47% strand | O53638 |
| D | L,D-transpeptidase 1 (EC 2.3.2.-) | protein | 192 | 10% helix, 45% strand | O53638 |
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1006 | 0.83 | 0.84 | 99 | empty |
| 2 | 658 | 0.67 | 0.76 | 84 | empty |
| 3 | 70 | 0.47 | 0.83 | 17 | empty |
| 4 | 211 | 0.47 | 0.74 | 33 | empty |
| 5 | 131 | 0.45 | 0.77 | 20 | empty |
Interfaces
4 interfaces between chains.
- B–D · 690 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 463 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 287 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 215 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5E5L · Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 1 at 1.89 Angstrom · the same entry in another collection · chain D against D, TM-score 1.00
- O53638 · AlphaFold monomer V2.0 prediction for L,D-transpeptidase 1 (O53638) · a predicted model of the same protein · chain C against A, TM-score 0.95
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 O53638
- Elsewhere: RCSB PDB 5E5L · PDBe 5E5L · UniProt O53638
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