Research workbench
Crystal structure of aspartate kinase from corynebacterium glutamicum in complex with threonine
Analyse Crystal structure of aspartate kinase from corynebacterium glutamicum in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AB2
- Type
- protein
- Length
- 4,297 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartokinase
- EC
- 2.7.2.4
- UniProt
- P26512
- Ligands
- THR
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 16 distinct chains · 38% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aspartokinase (EC 2.7.2.4) | protein | 386 | 39% helix, 24% strand | P26512 |
| B | Aspartokinase (EC 2.7.2.4) | protein | 160 | 32% helix, 35% strand | P26512 |
| C | Aspartokinase (EC 2.7.2.4) | protein | 380 | 40% helix, 24% strand | P26512 |
| D | Aspartokinase (EC 2.7.2.4) | protein | 152 | 33% helix, 36% strand | P26512 |
| E | Aspartokinase (EC 2.7.2.4) | protein | 383 | 40% helix, 25% strand | P26512 |
| F | Aspartokinase (EC 2.7.2.4) | protein | 155 | 34% helix, 35% strand | P26512 |
| G | Aspartokinase (EC 2.7.2.4) | protein | 383 | 42% helix, 25% strand | P26512 |
| H | Aspartokinase (EC 2.7.2.4) | protein | 155 | 36% helix, 36% strand | P26512 |
| I | Aspartokinase (EC 2.7.2.4) | protein | 377 | 38% helix, 25% strand | P26512 |
| J | Aspartokinase (EC 2.7.2.4) | protein | 152 | 32% helix, 39% strand | P26512 |
| K | Aspartokinase (EC 2.7.2.4) | protein | 382 | 41% helix, 25% strand | P26512 |
| L | Aspartokinase (EC 2.7.2.4) | protein | 152 | 28% helix, 36% strand | P26512 |
| M | Aspartokinase (EC 2.7.2.4) | protein | 380 | 39% helix, 23% strand | P26512 |
| N | Aspartokinase (EC 2.7.2.4) | protein | 155 | 34% helix, 35% strand | P26512 |
| O | Aspartokinase (EC 2.7.2.4) | protein | 386 | 41% helix, 23% strand | P26512 |
| P | Aspartokinase (EC 2.7.2.4) | protein | 159 | 32% helix, 35% strand | P26512 |
Ligands and binding sites
- THR · Threonine · ligand · 15 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
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 | 648 | 0.73 | 0.80 | 67 | empty |
| 2 | 599 | 0.73 | 0.81 | 65 | empty |
| 3 | 748 | 0.72 | 0.79 | 80 | empty |
| 4 | 695 | 0.72 | 0.79 | 79 | empty |
| 5 | 671 | 0.72 | 0.79 | 75 | empty |
Interfaces
32 interfaces between chains.
- O–P · 2694 Ų buried · 46 hydrogen bonds · protein-protein
- M–N · 2667 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 2612 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 2523 Ų buried · 36 hydrogen bonds · protein-protein
- G–H · 2515 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 3AB2 · Crystal structure of aspartate kinase from Corynebacterium glutamicum in complex with… · the same entry in another collection · chain I against I, 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 P26512
- Elsewhere: RCSB PDB 3AB2 · PDBe 3AB2 · UniProt P26512
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