MolNFT v1 · #114161 · protein
Crystal structure of HPIN1 ww domain (5-39) fused with maltose-binding protein
5B3Z · Peptidyl-prolyl cis-trans isomerase nima-interacting 1…: “Crystal structure of HPIN1 ww domain (5-39) fused with maltose-binding protein”. X-ray diffraction, 1 ligand (GLC), 11 pockets (best druggability 0.83). MolNFT v1 #114161 on…
- PDB
- 5B3Z
- Type
- protein
- Length
- 1,602 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-prolyl cis-trans isomerase nima-interacting 1, maltose-binding periplasmic…
- UniProt
- Q13526, P0AEX9
- Ligands
- GLC
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidyl-prolyl cis-trans isomerase nima-interacting 1, maltose-binding periplasmic protein | protein | 402 | 41% helix, 20% strand | Q13526, P0AEX9 |
| B | Peptidyl-prolyl cis-trans isomerase nima-interacting 1, maltose-binding periplasmic protein | protein | 400 | 41% helix, 22% strand | Q13526, P0AEX9 |
| C | Peptidyl-prolyl cis-trans isomerase nima-interacting 1, maltose-binding periplasmic protein | protein | 401 | 39% helix, 21% strand | Q13526, P0AEX9 |
| D | Peptidyl-prolyl cis-trans isomerase nima-interacting 1, maltose-binding periplasmic protein | protein | 399 | 41% helix, 20% strand | Q13526, P0AEX9 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1124 | 0.83 | 0.84 | 105 | empty |
| 2 | 1102 | 0.83 | 0.84 | 99 | empty |
| 3 | 1135 | 0.81 | 0.82 | 110 | empty |
| 4 | 1157 | 0.81 | 0.82 | 113 | empty |
| 5 | 383 | 0.73 | 0.84 | 35 | GLC |
Interfaces
5 interfaces between chains.
- A–B · 1125 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1118 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 901 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 889 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 121 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5B3Z · Crystal structure of hPin1 WW domain (5-39) fused with maltose-binding protein · the same entry in another collection · chain A against A, 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 Q13526
- Every structure of UniProt P0AEX9
- Elsewhere: RCSB PDB 5B3Z · PDBe 5B3Z · UniProt Q13526 · UniProt P0AEX9
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