MolNFT v1 · #121989 · protein
1.65 ångström crystal structure of triosephosphate isomerase (tim) from streptococcus pneumoniae
5IBX: “1.65 ångström crystal structure of triosephosphate isomerase (tim) from streptococcus pneumoniae”. X-ray diffraction, 1 ligand (NA), 20 pockets (best druggability 0.76). MolNFT v1 #121989 on GenesisL1: 3D structure, binding sites…
- PDB
- 5IBX
- Type
- protein
- Length
- 1,999 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Triosephosphate isomerase
- EC
- 5.3.1.1
- UniProt
- Q04JH4
- Ligands
- NA
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, F | Triosephosphate isomerase (EC 5.3.1.1) | protein | 250 | 46% helix, 16% strand | Q04JH4 |
| D | Triosephosphate isomerase (EC 5.3.1.1) | protein | 249 | 47% helix, 16% strand | Q04JH4 |
| E | Triosephosphate isomerase (EC 5.3.1.1) | protein | 251 | 45% helix, 16% strand | Q04JH4 |
| G | Triosephosphate isomerase (EC 5.3.1.1) | protein | 248 | 46% helix, 16% strand | Q04JH4 |
| H | Triosephosphate isomerase (EC 5.3.1.1) | protein | 251 | 48% helix, 16% strand | Q04JH4 |
Ligands and binding sites
- NA · Sodium ion · metal · 13 copies · chains A, B, C, E, D, 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 864 | 0.76 | 0.80 | 87 | NA |
| 2 | 958 | 0.75 | 0.78 | 87 | empty |
| 3 | 65 | 0.70 | 0.97 | 27 | empty |
| 4 | 62 | 0.70 | 0.97 | 28 | empty |
| 5 | 69 | 0.69 | 0.96 | 27 | empty |
Interfaces
15 interfaces between chains.
- D–G · 1631 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 1629 Ų buried · 24 hydrogen bonds · protein-protein
- B–H · 1626 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1622 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 481 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (artifact).
Compared structures
- 5IBX · 1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (TIM) from Streptococcus… · the same entry in another collection · chain H against H, TM-score 1.00
- Q04JH4 · AlphaFold monomer V2.0 prediction for triosephosphate isomerase (Q04JH4) · a predicted model of the same protein · chain G 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 Q04JH4
- Elsewhere: RCSB PDB 5IBX · PDBe 5IBX · UniProt Q04JH4
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