Research workbench
Alanine racemase [clostridium difficile 630]
Analyse Alanine racemase [clostridium difficile 630] in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LUS
- Type
- protein
- Length
- 1,498 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alanine racemase
- EC
- 5.1.1.1
- UniProt
- Q180W0
- Ligands
- TCE
- Pockets
- 19 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alanine racemase (EC 5.1.1.1) | protein | 362 | 34% helix, 25% strand | Q180W0 |
| B | Alanine racemase (EC 5.1.1.1) | protein | 374 | 33% helix, 27% strand | Q180W0 |
| C | Alanine racemase (EC 5.1.1.1) | protein | 382 | 33% helix, 26% strand | Q180W0 |
| D | Alanine racemase (EC 5.1.1.1) | protein | 380 | 33% helix, 26% strand | Q180W0 |
Ligands and binding sites
- TCE · 3,3',3''-phosphanetriyltripropanoic acid · ligand · chains B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.81 | 0.96 | 45 | empty |
| 2 | 184 | 0.80 | 0.95 | 44 | empty |
| 3 | 764 | 0.76 | 0.80 | 79 | empty |
| 4 | 567 | 0.67 | 0.77 | 93 | empty |
| 5 | 243 | 0.66 | 0.83 | 47 | empty |
Interfaces
3 interfaces between chains.
- C–D · 3325 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2804 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 614 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 modified (cofactor, carboxylation).
Compared structures
- 4LUS · alanine racemase [Clostridium difficile 630] · the same entry in another collection · chain C against C, 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 Q180W0
- Elsewhere: RCSB PDB 4LUS · PDBe 4LUS · UniProt Q180W0
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