Research workbench
Mgla bound to GDP in P1 tetrameric arrangement
Analyse Mgla bound to GDP in P1 tetrameric arrangement in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3T1T
- Type
- protein
- Length
- 754 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
- 7 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gliding protein mgla (EC 3.6.5.2) | protein | 193 | 37% helix, 25% strand | Q5SJ82 |
| B | Gliding protein mgla (EC 3.6.5.2) | protein | 192 | 36% helix, 27% strand | Q5SJ82 |
| C | Gliding protein mgla (EC 3.6.5.2) | protein | 178 | 37% helix, 25% strand | Q5SJ82 |
| D | Gliding protein mgla (EC 3.6.5.2) | protein | 191 | 33% helix, 28% strand | Q5SJ82 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 896 | 0.73 | 0.78 | 72 | GDP |
| 2 | 1036 | 0.72 | 0.76 | 93 | GDP |
| 3 | 528 | 0.68 | 0.78 | 60 | empty |
| 4 | 348 | 0.63 | 0.78 | 41 | empty |
| 5 | 87 | 0.49 | 0.82 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 325 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 238 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 236 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 214 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 93 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3T1T · MglA bound to GDP in P1 tetrameric arrangement · the same entry in another collection · chain A against A, 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 3T1T · PDBe 3T1T · UniProt Q5SJ82
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