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Crystal structure of LmrA ATP-binding domain
Analyse Crystal structure of LmrA ATP-binding domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MV5
- Type
- protein
- Length
- 967 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.1
- Source
- Lactococcus lactis
- Molecule
- Multidrug resistance ABC transporter ATP-binding and permease protein
- UniProt
- Q9CHL8
- Ligands
- ATP, ADP, MG
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · resolution 3.1 · 2 distinct chains · 32% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Multidrug resistance ABC transporter ATP-binding and permease protein | protein | 242 | 32% helix, 22% strand | Q9CHL8 |
| D | Multidrug resistance ABC transporter ATP-binding and permease protein | protein | 241 | 33% helix, 15% strand | Q9CHL8 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, D, B, C
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 474 | 0.80 | 0.87 | 57 | empty |
| 2 | 527 | 0.79 | 0.86 | 71 | empty |
| 3 | 1173 | 0.78 | 0.80 | 108 | ATP, ADP |
| 4 | 628 | 0.74 | 0.81 | 45 | empty |
| 5 | 505 | 0.72 | 0.81 | 76 | ADP, ATP |
Interfaces
5 interfaces between chains.
- A–B · 936 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 876 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 457 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 209 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 198 Ų buried · 2 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 Q9CHL8
- Elsewhere: RCSB PDB 1MV5 · PDBe 1MV5 · UniProt Q9CHL8
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