MolNFT v1 · #76496 · protein
The structural analysis of SIL1-bip complex reveals the mechanism for SIL1 to function as a novel nucleotide exchange factor
3QML · 78 kda glucose-regulated protein homolog: “The structural analysis of SIL1-bip complex reveals the mechanism for SIL1 to function as a novel nucleotide…”. X-ray diffraction, 2 ligands (MG, PO4), 13 pockets (best druggability 0.81).…
- PDB
- 3QML
- Type
- protein
- Length
- 1,282 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 78 kda glucose-regulated protein homolog; Nucleotide exchange factor SIL1
- UniProt
- P16474, Q08199
- Ligands
- MG, PO4
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 78 kda glucose-regulated protein homolog | protein | 377 | 40% helix, 28% strand | P16474 |
| B | 78 kda glucose-regulated protein homolog | protein | 370 | 37% helix, 25% strand | P16474 |
| C | Nucleotide exchange factor SIL1 | protein | 262 | 74% helix, 0% strand | Q08199 |
| D | Nucleotide exchange factor SIL1 | protein | 273 | 72% helix, 0% strand | Q08199 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, C
- PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1068 | 0.81 | 0.82 | 81 | PO4 |
| 2 | 1173 | 0.78 | 0.80 | 97 | PO4 |
| 3 | 996 | 0.76 | 0.79 | 89 | empty |
| 4 | 443 | 0.61 | 0.76 | 37 | empty |
| 5 | 427 | 0.60 | 0.76 | 37 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1497 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 1446 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 280 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 241 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3QML · The structural analysis of Sil1-Bip complex reveals the mechanism for Sil1 to function as… · the same entry in another collection · chain D against D, TM-score 1.00
- Q08199 · AlphaFold monomer V2.0 prediction for nucleotide exchange factor SIL1 (Q08199) · a predicted model of the same protein · chain D against A, TM-score 0.99
- P16474 · AlphaFold monomer V2.0 prediction for endoplasmic reticulum chaperone bip (P16474) · a predicted model of the same protein · chain A against A, TM-score 0.88
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 P16474
- Every structure of UniProt Q08199
- Elsewhere: RCSB PDB 3QML · PDBe 3QML · UniProt P16474 · UniProt Q08199
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