MolNFT v1 · #33976 · protein
Crystal structure of TT0538 protein from thermus thermophilus HB8
2D1C · Isocitrate dehydrogenase: “Crystal structure of TT0538 protein from thermus thermophilus HB8”. X-ray diffraction, 1 ligand (NAP), 10 pockets (best druggability 0.84). MolNFT v1 #33976 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2D1C
- Type
- protein
- Length
- 990 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase
- EC
- 1.1.1.42
- UniProt
- P33197
- Ligands
- NAP
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Isocitrate dehydrogenase (EC 1.1.1.42) | protein | 495 | 34% helix, 26% strand | P33197 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- CIT · Citric acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.84 | 0.92 | 38 | empty |
| 2 | 214 | 0.82 | 0.95 | 34 | empty |
| 3 | 477 | 0.75 | 0.84 | 49 | NAP, CIT |
| 4 | 488 | 0.72 | 0.82 | 52 | NAP, CIT |
| 5 | 356 | 0.59 | 0.76 | 48 | empty |
Interfaces
1 interface between chains.
- A–B · 5744 Ų buried · 108 hydrogen bonds · protein-protein
Compared structures
- 2D1C · Crystal Structure Of TT0538 protein from Thermus thermophilus HB8 · the same entry in another collection · chain A against A, TM-score 1.00
- P33197 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NADP] (P33197) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P33197
- Elsewhere: RCSB PDB 2D1C · PDBe 2D1C · UniProt P33197
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