Research workbench
Inward facing conformations of the metni methionine ABC transporter: CY5 semet soak crystal form
Analyse Inward facing conformations of the metni methionine ABC transporter: CY5 semet… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TUZ
- Type
- protein
- Length
- 2,233 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-methionine transport system permease protein meti; Methionine import ATP-binding…
- EC
- 3.6.3.-
- UniProt
- P31547, P30750
- Ligands
- MSE, ADP
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 50% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, F | D-methionine transport system permease protein meti | protein | 216 | 79% helix, 0% strand | P31547 |
| C | Methionine import ATP-binding protein metn (EC 3.6.3.-) | protein | 344 | 36% helix, 28% strand | P30750 |
| D, G | Methionine import ATP-binding protein metn (EC 3.6.3.-) | protein | 343 | 37% helix, 27% strand | P30750 |
| E | D-methionine transport system permease protein meti | protein | 215 | 83% helix, 0% strand | P31547 |
| H | Methionine import ATP-binding protein metn (EC 3.6.3.-) | protein | 340 | 37% helix, 28% strand | P30750 |
Ligands and binding sites
- MSE · Selenomethionine · ligand · 4 copies · chains C, D, G, H
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains C, D, G, H
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 | 701 | 0.74 | 0.80 | 52 | empty |
| 2 | 617 | 0.74 | 0.81 | 61 | empty |
| 3 | 55 | 0.73 | 0.99 | 21 | MSE |
| 4 | 57 | 0.73 | 0.99 | 21 | MSE |
| 5 | 621 | 0.64 | 0.75 | 69 | empty |
Interfaces
10 interfaces between chains.
- E–F · 1529 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 1422 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1382 Ų buried · 5 hydrogen bonds · protein-protein
- G–H · 1340 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 991 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3TUZ · Inward facing conformations of the MetNI methionine ABC transporter: CY5 SeMet soak… · the same entry in another collection · chain H against H, 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 E against A, TM-score 0.99
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 P31547
- Every structure of UniProt P30750
- Elsewhere: RCSB PDB 3TUZ · PDBe 3TUZ · UniProt P31547 · UniProt P30750
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