Research workbench
Crystal structure of the bip nbd and manf sap complex
Analyse Crystal structure of the bip nbd and manf sap complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H9U
- Type
- protein
- Length
- 419 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoplasmic reticulum chaperone bip; Mesencephalic astrocyte-derived neurotrophic factor
- EC
- 3.6.4.10
- UniProt
- G3I8R9, Q9CXI5
- Ligands
- MLT, NA
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoplasmic reticulum chaperone bip (EC 3.6.4.10) | protein | 379 | 41% helix, 27% strand | G3I8R9 |
| B | Mesencephalic astrocyte-derived neurotrophic factor | protein | 40 | 53% helix, 3% strand | Q9CXI5 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 360 | 0.73 | 0.85 | 55 | NA |
| 2 | 225 | 0.52 | 0.76 | 28 | empty |
| 3 | 74 | 0.38 | 0.78 | 19 | empty |
| 4 | 52 | 0.37 | 0.80 | 18 | empty |
| 5 | 72 | 0.36 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 582 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6H9U · Crystal structure of the BiP NBD and MANF SAP complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q9CXI5 · AlphaFold monomer V2.0 prediction for mesencephalic astrocyte-derived neurotrophic factor… · a predicted model of the same protein · chain B against A, TM-score 0.88
- G3I8R9 · AlphaFold monomer V2.0 prediction for endoplasmic reticulum chaperone bip (G3I8R9) · a predicted model of the same protein · chain A against A, TM-score 0.84
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 G3I8R9
- Every structure of UniProt Q9CXI5
- Elsewhere: RCSB PDB 6H9U · PDBe 6H9U · UniProt G3I8R9 · UniProt Q9CXI5
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