MolNFT v1 · #106414 · protein
The crystal structure of D-alanyl-D-alanine carboxypeptidase from mycobacterium tuberculosis H37RV
4RYE: “The crystal structure of D-alanyl-D-alanine carboxypeptidase from mycobacterium tuberculosis H37RV”. X-ray diffraction, 8 pockets (best druggability 0.79). MolNFT v1 #106414 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4RYE
- Type
- protein
- Length
- 1,056 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-alanyl-D-alanine carboxypeptidase
- UniProt
- I6Y204
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | D-alanyl-D-alanine carboxypeptidase | protein | 264 | 34% helix, 26% strand | I6Y204 |
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 373 | 0.79 | 0.89 | 54 | empty |
| 2 | 427 | 0.78 | 0.87 | 63 | empty |
| 3 | 220 | 0.63 | 0.82 | 43 | empty |
| 4 | 201 | 0.61 | 0.82 | 38 | empty |
| 5 | 122 | 0.42 | 0.76 | 28 | empty |
Interfaces
4 interfaces between chains.
- A–B · 610 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 603 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 355 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 346 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 24 modified, 1 disulfide (engineered, disulfide).
Compared structures
- 4RYE · The crystal structure of D-ALANYL-D-ALANINE CARBOXYPEPTIDASE from Mycobacterium… · the same entry in another collection · chain D against D, TM-score 1.00
- I6Y204 · AlphaFold monomer V2.0 prediction for D-alanyl-D-alanine carboxypeptidase DACB2 (I6Y204) · a predicted model of the same protein · chain B against A, 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 I6Y204
- Elsewhere: RCSB PDB 4RYE · PDBe 4RYE · UniProt I6Y204
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