Research workbench
Crystal structure of the escherichia COLI atpgs-bound metni methionine ABC transporter in complex with its metq binding protein
Analyse Crystal structure of the escherichia COLI atpgs-bound metni methionine ABC… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CVL
- Type
- protein
- Length
- 1,343 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metn nucleotide-binding subunit; Meti transmembrane subunit; Metq periplasmic binding…
- EC
- 3.6.3.-
- UniProt
- P30750, P31547, P28635
- Ligands
- AGS, HG, IOD
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Metn nucleotide-binding subunit (EC 3.6.3.-) | protein | 343 | 38% helix, 30% strand | P30750 |
| A, B | Meti transmembrane subunit | protein | 215 | 84% helix, 0% strand | P31547 |
| D | Metn nucleotide-binding subunit (EC 3.6.3.-) | protein | 344 | 37% helix, 31% strand | P30750 |
| E | Metq periplasmic binding protein | protein | 226 | 36% helix, 17% strand | P28635 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 2 copies · chains C, D
- HG · Mercury (II) ion · metal · 3 copies · chains C, D
- IOD · Iodide ion · ion · 2 copies · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 834 | 0.87 | 0.89 | 100 | empty |
| 2 | 1060 | 0.84 | 0.85 | 136 | HG, IOD |
| 3 | 287 | 0.84 | 0.94 | 38 | empty |
| 4 | 774 | 0.77 | 0.81 | 93 | AGS |
| 5 | 68 | 0.73 | 0.97 | 25 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2847 Ų buried · 55 hydrogen bonds · protein-protein
- A–B · 1897 Ų buried · 10 hydrogen bonds · protein-protein
- C–A · 872 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 869 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 851 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6CVL · Crystal structure of the Escherichia coli ATPgS-bound MetNI methionine ABC transporter in… · the same entry in another collection · chain E against E, TM-score 1.00
- P31547 · AlphaFold monomer V2.0 prediction for D-methionine transport system permease protein meti… · a predicted model of the same protein · chain A against A, TM-score 0.93
- P30750 · AlphaFold monomer V2.0 prediction for methionine import ATP-binding protein metn (P30750) · a predicted model of the same protein · chain D against A, TM-score 0.91
- P28635 · AlphaFold monomer V2.0 prediction for D-methionine-binding lipoprotein metq (P28635) · a predicted model of the same protein · chain E against A, TM-score 0.82
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 P30750
- Every structure of UniProt P31547
- Every structure of UniProt P28635
- Elsewhere: RCSB PDB 6CVL · PDBe 6CVL · UniProt P30750 · UniProt P31547 · UniProt P28635
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