MolNFT v1 · #62176 · protein
Crystal structure of dlta: implications for the reaction mechanism of non-ribosomal peptide synthetase (nrps) adenylation domains
3E7X · D-alanine--POLY(PHOSPHORIBITOL) ligase subunit 1: “Crystal structure of dlta: implications for the reaction mechanism of non-ribosomal peptide synthetase (nrps)…”. X-ray diffraction, 1 ligand (AMP), 3 pockets (best druggability…
- PDB
- 3E7X
- Type
- protein
- Length
- 508 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-alanine--POLY(PHOSPHORIBITOL) ligase subunit 1
- EC
- 6.1.1.13
- UniProt
- P39581
- Ligands
- AMP
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanine--POLY(PHOSPHORIBITOL) ligase subunit 1 (EC 6.1.1.13) | protein | 508 | 33% helix, 27% strand | P39581 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 792 | 0.79 | 0.82 | 91 | AMP |
| 2 | 157 | 0.45 | 0.76 | 23 | empty |
| 3 | 53 | 0.28 | 0.75 | 12 | empty |
Compared structures
- 3E7X · Crystal structure of DLTA: implications for the reaction mechanism of non-ribosomal… · the same entry in another collection · chain A against A, TM-score 1.00
- P39581 · AlphaFold monomer V2.0 prediction for D-alanine--D-alanyl carrier protein ligase (P39581) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P39581
- Elsewhere: RCSB PDB 3E7X · PDBe 3E7X · UniProt P39581
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