Research workbench
Complex of mycobacterium smegmatis trehalose synthase with maltokinase
Analyse Complex of mycobacterium smegmatis trehalose synthase with maltokinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JY7
- Type
- protein
- Length
- 7,428 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trehalose SYNTHASE/AMYLASE tres; Maltokinase
- EC
- 3.2.1.1, 5.4.99.16, 2.7.1.175
- UniProt
- A0R6E0, A0R6D9
- Ligands
- CA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 11 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trehalose SYNTHASE/AMYLASE tres (EC 3.2.1.1, 5.4.99.16) | protein | 565 | 31% helix, 18% strand | A0R6E0 |
| B, D, F, G | Trehalose SYNTHASE/AMYLASE tres (EC 3.2.1.1, 5.4.99.16) | protein | 571 | 31% helix, 18% strand | A0R6E0 |
| C | Trehalose SYNTHASE/AMYLASE tres (EC 3.2.1.1, 5.4.99.16) | protein | 569 | 32% helix, 18% strand | A0R6E0 |
| E | Trehalose SYNTHASE/AMYLASE tres (EC 3.2.1.1, 5.4.99.16) | protein | 549 | 32% helix, 18% strand | A0R6E0 |
| H | Trehalose SYNTHASE/AMYLASE tres (EC 3.2.1.1, 5.4.99.16) | protein | 544 | 33% helix, 18% strand | A0R6E0 |
| I, J | Maltokinase (EC 2.7.1.175) | protein | 435 | 41% helix, 19% strand | A0R6D9 |
| K | Maltokinase (EC 2.7.1.175) | protein | 353 | 49% helix, 16% strand | A0R6D9 |
| L | Maltokinase (EC 2.7.1.175) | protein | 436 | 42% helix, 20% strand | A0R6D9 |
| M | Maltokinase (EC 2.7.1.175) | protein | 431 | 44% helix, 19% strand | A0R6D9 |
| N | Maltokinase (EC 2.7.1.175) | protein | 349 | 49% helix, 15% strand | A0R6D9 |
| O, P | Maltokinase (EC 2.7.1.175) | protein | 239 | 62% helix, 8% strand | A0R6D9 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 972 | 0.87 | 0.88 | 110 | empty |
| 2 | 527 | 0.85 | 0.91 | 37 | empty |
| 3 | 1058 | 0.85 | 0.86 | 116 | empty |
| 4 | 1028 | 0.85 | 0.86 | 106 | empty |
| 5 | 542 | 0.84 | 0.90 | 40 | empty |
Interfaces
31 interfaces between chains.
- G–H · 1282 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 1243 Ų buried · 9 hydrogen bonds · protein-protein
- B–I · 1032 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 967 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 943 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5JY7 · Complex of Mycobacterium smegmatis trehalose synthase with maltokinase · the same entry in another collection · chain E against E, 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 A0R6E0
- Every structure of UniProt A0R6D9
- Elsewhere: RCSB PDB 5JY7 · PDBe 5JY7 · UniProt A0R6E0 · UniProt A0R6D9
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