MolNFT v1 · #90351 · protein
Crystal structure of D-alanine-D-alanine ligase B from burkholderia pseudomallei
4EGQ · D-alanine--D-alanine ligase: “Crystal structure of D-alanine-D-alanine ligase B from burkholderia pseudomallei”. X-ray diffraction, 6 pockets (best druggability 0.74). MolNFT v1 #90351 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4EGQ
- Type
- protein
- Length
- 1,180 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-alanine--D-alanine ligase
- EC
- 6.3.2.4
- UniProt
- Q3JNE1
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 288 | 39% helix, 21% strand | Q3JNE1 |
| B | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 302 | 38% helix, 21% strand | Q3JNE1 |
| C | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 302 | 41% helix, 22% strand | Q3JNE1 |
| D | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 288 | 39% helix, 22% strand | Q3JNE1 |
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 954 | 0.74 | 0.77 | 87 | empty |
| 2 | 132 | 0.42 | 0.75 | 20 | empty |
| 3 | 93 | 0.36 | 0.75 | 23 | empty |
| 4 | 89 | 0.36 | 0.75 | 17 | empty |
| 5 | 127 | 0.36 | 0.73 | 18 | empty |
Interfaces
2 interfaces between chains.
- B–C · 428 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 55 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4EGQ · Crystal structure of D-alanine-D-alanine ligase B from Burkholderia pseudomallei · the same entry in another collection · chain D against D, TM-score 1.00
- Q3JNE1 · AlphaFold monomer V2.0 prediction for D-alanine--D-alanine ligase (Q3JNE1) · a predicted model of the same protein · chain C against A, TM-score 0.83
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 Q3JNE1
- Elsewhere: RCSB PDB 4EGQ · PDBe 4EGQ · UniProt Q3JNE1
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