Research workbench
Crystal structure of a membrane protein, crystal form II
Analyse Crystal structure of a membrane protein, crystal form II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BUH
- Type
- protein
- Length
- 1,972 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-alanyl carrier protein; D-alanyl transfer protein dltb
- UniProt
- Q5M0A6, Q5M4V4
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, G | D-alanyl carrier protein | protein | 79 | 48% helix, 3% strand | Q5M0A6 |
| C, D, F, H | D-alanyl transfer protein dltb | protein | 414 | 74% helix, 0% strand | Q5M4V4 |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.71 | 0.85 | 29 | empty |
| 2 | 663 | 0.70 | 0.77 | 53 | empty |
| 3 | 196 | 0.70 | 0.87 | 25 | empty |
| 4 | 544 | 0.69 | 0.78 | 41 | empty |
| 5 | 516 | 0.69 | 0.79 | 38 | empty |
Interfaces
10 interfaces between chains.
- G–H · 826 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 803 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 803 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 799 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 514 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 6BUH · Crystal structure of a membrane protein, crystal form II · the same entry in another collection · chain E against E, TM-score 1.00
- Q5M4V4 · AlphaFold monomer V2.0 prediction for teichoic acid D-alanyltransferase (Q5M4V4) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 Q5M0A6
- Every structure of UniProt Q5M4V4
- Elsewhere: RCSB PDB 6BUH · PDBe 6BUH · UniProt Q5M0A6 · UniProt Q5M4V4
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