Research workbench
Mgla bound to GDP in P2(1) tetrameric arrangement
Analyse Mgla bound to GDP in P2(1) tetrameric arrangement in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3T1V
- Type
- protein
- Length
- 766 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gliding protein mgla
- EC
- 3.6.5.2
- UniProt
- Q5SJ82
- Ligands
- GDP
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Gliding protein mgla (EC 3.6.5.2) | protein | 192 | 35% helix, 26% strand | Q5SJ82 |
| C | Gliding protein mgla (EC 3.6.5.2) | protein | 190 | 33% helix, 27% strand | Q5SJ82 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1107 | 0.81 | 0.82 | 95 | GDP |
| 2 | 1159 | 0.71 | 0.75 | 110 | GDP |
| 3 | 91 | 0.44 | 0.79 | 16 | empty |
| 4 | 57 | 0.37 | 0.79 | 19 | empty |
| 5 | 56 | 0.37 | 0.79 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–B · 586 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 548 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 208 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 186 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 143 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3T1V · MglA bound to GDP in P2(1) tetrameric arrangement · the same entry in another collection · chain B against B, TM-score 1.00
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 Q5SJ82
- Elsewhere: RCSB PDB 3T1V · PDBe 3T1V · UniProt Q5SJ82
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