Research workbench
Crystal structure of mycobacterium abscessus L,D-transpeptidase 2
Analyse Crystal structure of mycobacterium abscessus L,D-transpeptidase 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UWV
- Type
- protein
- Length
- 2,011 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L,D-transpeptidase 2
- UniProt
- B1MMQ4
- Pockets
- 15 · best druggability 0.73
Structure
x-ray diffraction · 6 distinct chains · 8% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | L,D-transpeptidase 2 | protein | 334 | 8% helix, 45% strand | B1MMQ4 |
| A | L,D-transpeptidase 2 | protein | 333 | 8% helix, 42% strand | B1MMQ4 |
| D | L,D-transpeptidase 2 | protein | 334 | 8% helix, 45% strand | B1MMQ4 |
| E | L,D-transpeptidase 2 | protein | 335 | 7% helix, 39% strand | B1MMQ4 |
| C | L,D-transpeptidase 2 | protein | 338 | 8% helix, 41% strand | B1MMQ4 |
| F | L,D-transpeptidase 2 | protein | 337 | 9% helix, 43% strand | B1MMQ4 |
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 819 | 0.73 | 0.78 | 84 | empty |
| 2 | 437 | 0.63 | 0.77 | 57 | empty |
| 3 | 495 | 0.61 | 0.75 | 72 | empty |
| 4 | 411 | 0.58 | 0.75 | 48 | empty |
| 5 | 360 | 0.53 | 0.73 | 46 | empty |
Interfaces
5 interfaces between chains.
- E–C · 677 Ų buried · 3 hydrogen bonds · protein-protein
- B–F · 643 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 541 Ų buried · 6 hydrogen bonds · protein-protein
- B–A · 455 Ų buried · 11 hydrogen bonds · protein-protein
- C–F · 356 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5UWV · Crystal structure of Mycobacterium abscessus L,D-transpeptidase 2 · the same entry in another collection · chain B against B, TM-score 1.00
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 B1MMQ4
- Elsewhere: RCSB PDB 5UWV · PDBe 5UWV · UniProt B1MMQ4
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