Research workbench
Structure of human triose phosphate isomerase R189A
Analyse Structure of human triose phosphate isomerase R189A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NLH
- Type
- protein
- Length
- 1,934 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Triosephosphate isomerase
- EC
- 5.3.1.1
- UniProt
- P60174
- Ligands
- NA, BR, PO4
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Triosephosphate isomerase (EC 5.3.1.1) | protein | 244 | 45% helix, 17% strand | P60174 |
| E | Triosephosphate isomerase (EC 5.3.1.1) | protein | 238 | 45% helix, 18% strand | P60174 |
| B, D, G | Triosephosphate isomerase (EC 5.3.1.1) | protein | 245 | 45% helix, 17% strand | P60174 |
| C, F | Triosephosphate isomerase (EC 5.3.1.1) | protein | 239 | 45% helix, 17% strand | P60174 |
| H | Triosephosphate isomerase (EC 5.3.1.1) | protein | 239 | 45% helix, 17% strand | P60174 |
Ligands and binding sites
- NA · Sodium ion · metal · 20 copies · chains A, E, B, C, D, F, G, H
- BR · Bromide ion · ion · 4 copies · chains E, C, F, H
- PO4 · Phosphate ion · ion · 4 copies · chains E, C, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 781 | 0.80 | 0.83 | 91 | empty |
| 2 | 53 | 0.69 | 0.98 | 15 | NA |
| 3 | 53 | 0.69 | 0.98 | 16 | empty |
| 4 | 55 | 0.69 | 0.98 | 16 | empty |
| 5 | 741 | 0.66 | 0.74 | 73 | BR, PO4 |
Interfaces
13 interfaces between chains.
- D–F · 1801 Ų buried · 43 hydrogen bonds · protein-protein
- B–C · 1795 Ų buried · 44 hydrogen bonds · protein-protein
- G–H · 1794 Ų buried · 42 hydrogen bonds · protein-protein
- A–E · 1784 Ų buried · 40 hydrogen bonds · protein-protein
- B–D · 416 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
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 P60174
- Elsewhere: RCSB PDB 6NLH · PDBe 6NLH · UniProt P60174
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