MolNFT v1 · #136955 · protein
Crystal structure of ERP29 D-domain in complex with the P-domain of calmegin
5V8Z · Endoplasmic reticulum resident protein 29: “Crystal structure of ERP29 D-domain in complex with the P-domain of calmegin”. X-ray diffraction, 3 pockets (best druggability 0.59). MolNFT v1 #136955 on GenesisL1: 3D structure, binding…
- PDB
- 5V8Z
- Type
- protein
- Length
- 249 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoplasmic reticulum resident protein 29; Calmegin
- UniProt
- P30040, E2RA18
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 73% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoplasmic reticulum resident protein 29 | protein | 97 | 81% helix, 0% strand | P30040 |
| B, D | Calmegin | protein | 27 | 15% helix, 15% strand | E2RA18 |
| C | Endoplasmic reticulum resident protein 29 | protein | 98 | 82% helix, 0% strand | P30040 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.59 | 0.86 | 21 | empty |
| 2 | 74 | 0.36 | 0.77 | 20 | empty |
| 3 | 83 | 0.35 | 0.75 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–C · 882 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 699 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 658 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5V8Z · Crystal structure of ERp29 D-domain in complex with the P-domain of calmegin · the same entry in another collection · chain D against D, TM-score 1.00
- P30040 · AlphaFold monomer V2.0 prediction for endoplasmic reticulum resident protein 29 (P30040) · a predicted model of the same protein · chain C against A, TM-score 0.98
- E2RA18 · AlphaFold monomer V2.0 prediction for calmegin (E2RA18) · a predicted model of the same protein · chain B against A, TM-score 0.78
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 P30040
- Every structure of UniProt E2RA18
- Elsewhere: RCSB PDB 5V8Z · PDBe 5V8Z · UniProt P30040 · UniProt E2RA18
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