Research workbench
Lolcde in complex with AMP-pnp in the closed nbd state
Analyse Lolcde in complex with AMP-pnp in the closed nbd state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ARK
- Type
- protein
- Length
- 1,243 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipoprotein-releasing ABC transporter permease subunit lolc; Lipoprotein-releasing system…
- EC
- 7.6.2.-
- UniProt
- A0A4S5ATA9, P75958, P75957
- Ligands
- ANP, MG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 28% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Lipoprotein-releasing ABC transporter permease subunit lolc | protein | 386 | 29% helix, 12% strand | A0A4S5ATA9 |
| E | Lipoprotein-releasing system transmembrane protein lole | protein | 405 | 29% helix, 14% strand | P75958 |
| D, F | Lipoprotein-releasing system ATP-binding protein lold (EC 7.6.2.-) | protein | 226 | 23% helix, 16% strand | P75957 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains C, D, F, E
- MG · Magnesium ion · metal · 2 copies · chains D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 670 | 0.87 | 0.91 | 111 | empty |
| 2 | 556 | 0.81 | 0.87 | 66 | empty |
| 3 | 256 | 0.78 | 0.91 | 36 | empty |
| 4 | 266 | 0.77 | 0.90 | 43 | empty |
| 5 | 307 | 0.74 | 0.87 | 37 | ANP, MG |
Interfaces
6 interfaces between chains.
- C–E · 3516 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1361 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1151 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 1018 Ų buried · 9 hydrogen bonds · protein-protein
- E–D · 112 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7ARK · LolCDE in complex with AMP-PNP in the closed NBD state · the same entry in another collection · chain C against C, TM-score 1.00
- P75957 · AlphaFold monomer V2.0 prediction for lipoprotein-releasing system ATP-binding protein… · a predicted model of the same protein · chain D against A, TM-score 0.89
- P75958 · AlphaFold monomer V2.0 prediction for lipoprotein-releasing system transmembrane protein… · a predicted model of the same protein · chain E against A, TM-score 0.74
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 A0A4S5ATA9
- Every structure of UniProt P75958
- Every structure of UniProt P75957
- Elsewhere: RCSB PDB 7ARK · PDBe 7ARK · UniProt A0A4S5ATA9 · UniProt P75958 · UniProt P75957
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