Research workbench
Choline binding domain of the major autolysin (C-lyta) from streptococcus pneumoniae
Analyse Choline binding domain of the major autolysin (C-lyta) from streptococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GVM
- Type
- protein
- Length
- 769 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Autolysin
- EC
- 3.5.1.28
- UniProt
- P06653
- Ligands
- CHT, DDQ
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 5 distinct chains · 0% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Autolysin (EC 3.5.1.28) | protein | 127 | 0% helix, 43% strand | P06653 |
| B | Autolysin (EC 3.5.1.28) | protein | 133 | 0% helix, 41% strand | P06653 |
| D | Autolysin (EC 3.5.1.28) | protein | 125 | 0% helix, 40% strand | P06653 |
| E | Autolysin (EC 3.5.1.28) | protein | 123 | 2% helix, 28% strand | P06653 |
| F | Autolysin (EC 3.5.1.28) | protein | 134 | 0% helix, 43% strand | P06653 |
Ligands and binding sites
- CHT · Choline ion · ligand · 20 copies · chains A, B, C, D, E, F
- DDQ · Decylamine-N,N-dimethyl-N-oxide · ligand · chains F
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 580 | 0.66 | 0.76 | 51 | empty |
| 2 | 249 | 0.48 | 0.73 | 31 | empty |
| 3 | 142 | 0.40 | 0.74 | 23 | empty |
| 4 | 128 | 0.36 | 0.72 | 26 | CHT |
| 5 | 57 | 0.30 | 0.75 | 9 | CHT |
Interfaces
8 interfaces between chains.
- E–F · 1028 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 978 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 975 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 238 Ų buried · 1 hydrogen bond · protein-protein
- C–F · 192 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1GVM · Choline binding domain of the major autolysin (C-lyta) from streptococcus pneumoniae · the same entry in another collection · chain F against F, TM-score 1.00
- P06653 · AlphaFold monomer V2.0 prediction for autolysin (P06653) · a predicted model of the same protein · chain E against A, TM-score 0.95
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 P06653
- Elsewhere: RCSB PDB 1GVM · PDBe 1GVM · UniProt P06653
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