MolNFT v1 · #1806 · protein
Alanine racemase complexed with alanine phosphonate
1BD0: “Alanine racemase complexed with alanine phosphonate”. X-ray diffraction, 1 ligand (IN5), 9 pockets (best druggability 0.76). MolNFT v1 #1806 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1BD0
- Type
- protein
- Length
- 761 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alanine racemase
- EC
- 5.1.1.1
- UniProt
- P10724
- Ligands
- IN5
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alanine racemase (EC 5.1.1.1) | protein | 381 | 33% helix, 27% strand | P10724 |
| B | Alanine racemase (EC 5.1.1.1) | protein | 380 | 33% helix, 27% strand | P10724 |
Ligands and binding sites
- IN5 · {1-[(3-hydroxy-methyl-5-phosphonooxy-methyl-pyridin-4-ylmethyl)-amino]-ethyl}-phosphonic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 294 | 0.76 | 0.88 | 52 | IN5 |
| 2 | 260 | 0.75 | 0.88 | 47 | IN5 |
| 3 | 334 | 0.74 | 0.86 | 78 | empty |
| 4 | 102 | 0.56 | 0.85 | 25 | empty |
| 5 | 93 | 0.52 | 0.83 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 3256 Ų buried · 52 hydrogen bonds · protein-protein
Compared structures
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 P10724
- Elsewhere: RCSB PDB 1BD0 · PDBe 1BD0 · UniProt P10724
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