MolNFT v1 · #144463 · protein
Crystal structure of a membrane protein, crystal form I
6BUG · D-alanyl carrier protein: “Crystal structure of a membrane protein, crystal form I”. X-ray diffraction, 20 pockets (best druggability 0.73). MolNFT v1 #144463 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6BUG
- Type
- protein
- Length
- 1,893 residues
- Chains
- 7
- 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 0.73
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | D-alanyl carrier protein | protein | 79 | 41% helix, 3% strand | Q5M0A6 |
| C, D, F, G | D-alanyl transfer protein dltb | protein | 414 | 73% helix, 0% strand | Q5M4V4 |
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 513 | 0.73 | 0.81 | 60 | empty |
| 2 | 877 | 0.72 | 0.77 | 66 | empty |
| 3 | 354 | 0.72 | 0.84 | 48 | empty |
| 4 | 777 | 0.71 | 0.76 | 61 | empty |
| 5 | 577 | 0.70 | 0.78 | 43 | empty |
Interfaces
9 interfaces between chains.
- B–D · 817 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 776 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 772 Ų buried · 6 hydrogen bonds · protein-protein
- D–G · 484 Ų buried · 5 hydrogen bonds · protein-protein
- C–F · 414 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (phosphorylation).
Compared structures
- 6BUG · Crystal structure of a membrane protein, crystal form I · the same entry in another collection · chain G against G, TM-score 1.00
- Q5M4V4 · AlphaFold monomer V2.0 prediction for teichoic acid D-alanyltransferase (Q5M4V4) · a predicted model of the same protein · chain G against A, TM-score 0.98
- Q5M0A6 · AlphaFold monomer V2.0 prediction for D-alanyl carrier protein (Q5M0A6) · a predicted model of the same protein · chain E against A, TM-score 0.91
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 6BUG · PDBe 6BUG · UniProt Q5M0A6 · UniProt Q5M4V4
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