MolNFT v1 · #38711 · protein
Crystal structure of triosephosphate isomerase (tim) from methanocaldococcus jannaschii
2H6R: “Crystal structure of triosephosphate isomerase (tim) from methanocaldococcus jannaschii”. X-ray diffraction, 15 pockets (best druggability 0.76). MolNFT v1 #38711 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2H6R
- Type
- protein
- Length
- 1,625 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Triosephosphate isomerase
- EC
- 5.3.1.1
- UniProt
- Q58923
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 8 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Triosephosphate isomerase (EC 5.3.1.1) | protein | 203 | 41% helix, 18% strand | Q58923 |
| B | Triosephosphate isomerase (EC 5.3.1.1) | protein | 209 | 38% helix, 19% strand | Q58923 |
| C | Triosephosphate isomerase (EC 5.3.1.1) | protein | 204 | 38% helix, 19% strand | Q58923 |
| D | Triosephosphate isomerase (EC 5.3.1.1) | protein | 200 | 41% helix, 19% strand | Q58923 |
| E | Triosephosphate isomerase (EC 5.3.1.1) | protein | 207 | 39% helix, 19% strand | Q58923 |
| F | Triosephosphate isomerase (EC 5.3.1.1) | protein | 201 | 38% helix, 19% strand | Q58923 |
| G | Triosephosphate isomerase (EC 5.3.1.1) | protein | 200 | 39% helix, 18% strand | Q58923 |
| H | Triosephosphate isomerase (EC 5.3.1.1) | protein | 201 | 39% helix, 19% strand | Q58923 |
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 932 | 0.76 | 0.79 | 74 | empty |
| 2 | 500 | 0.68 | 0.79 | 48 | empty |
| 3 | 442 | 0.56 | 0.73 | 49 | empty |
| 4 | 404 | 0.55 | 0.73 | 52 | empty |
| 5 | 105 | 0.54 | 0.84 | 22 | empty |
Interfaces
11 interfaces between chains.
- G–H · 1525 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 1484 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 1484 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1456 Ų buried · 28 hydrogen bonds · protein-protein
- F–H · 855 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2H6R · Crystal Structure of triosephosphate isomerase (TIM) from Methanocaldococcus jannaschii · the same entry in another collection · chain H against H, TM-score 1.00
- Q58923 · AlphaFold monomer V2.0 prediction for triosephosphate isomerase (Q58923) · a predicted model of the same protein · chain G against A, TM-score 0.99
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 Q58923
- Elsewhere: RCSB PDB 2H6R · PDBe 2H6R · UniProt Q58923
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