Research workbench
Crystal structure of the ADP-mg-bound E. COLI malk (crystallized with ADP-mg)
Analyse Crystal structure of the ADP-mg-bound E. COLI malk (crystallized with ADP-mg) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AWO
- Type
- protein
- Length
- 1,408 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MALTOSE/MALTODEXTRIN import ATP-binding protein malk
- EC
- 3.6.3.19
- UniProt
- P68187
- Ligands
- ADP, MG
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MALTOSE/MALTODEXTRIN import ATP-binding protein malk (EC 3.6.3.19) | protein | 372 | 22% helix, 34% strand | P68187 |
| B | MALTOSE/MALTODEXTRIN import ATP-binding protein malk (EC 3.6.3.19) | protein | 374 | 25% helix, 33% strand | P68187 |
| C | MALTOSE/MALTODEXTRIN import ATP-binding protein malk (EC 3.6.3.19) | protein | 363 | 23% helix, 31% strand | P68187 |
| D | MALTOSE/MALTODEXTRIN import ATP-binding protein malk (EC 3.6.3.19) | protein | 299 | 18% helix, 41% strand | P68187 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains B, A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 782 | 0.83 | 0.86 | 73 | empty |
| 2 | 939 | 0.83 | 0.85 | 89 | empty |
| 3 | 308 | 0.75 | 0.88 | 35 | empty |
| 4 | 426 | 0.60 | 0.75 | 50 | empty |
| 5 | 251 | 0.54 | 0.76 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1602 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1501 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 432 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 90 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 32 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2AWO · Crystal structure of the ADP-Mg-bound E. Coli MALK (Crystallized with ADP-Mg) · the same entry in another collection · chain D against D, TM-score 1.00
- P68187 · AlphaFold monomer V2.0 prediction for MALTOSE/MALTODEXTRIN import ATP-binding protein… · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P68187
- Elsewhere: RCSB PDB 2AWO · PDBe 2AWO · UniProt P68187
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