Research workbench
Model of retromer-VPS5 complex assembled on membrane.
Analyse Model of retromer-VPS5 complex assembled on membrane. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H7W
- Type
- protein
- Length
- 6,188 residues
- Chains
- 20
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar protein sorting-associated protein 26-like protein; Putative vacuolar protein…
- UniProt
- G0S0E6, G0SH11, G0RZB5, G0S709
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · 6 distinct chains · 56% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| J, C | Vacuolar protein sorting-associated protein 26-like protein | protein | 292 | 2% helix, 62% strand | G0S0E6 |
| B, A, G, E, P, N, H, F | Putative vacuolar protein sorting-associated protein | protein | 349 | 72% helix, 8% strand | G0SH11 |
| D, K, V, L | Putative vacuolar protein sorting-associated protein | protein | 129 | 39% helix, 21% strand | G0SH11 |
| O, M | Putative vacuolar protein sorting-associated protein | protein | 220 | 92% helix, 0% strand | G0SH11 |
| S, T | Vacuolar protein sorting-associated protein 29 | protein | 184 | 15% helix, 36% strand | G0RZB5 |
| Q, R | Vacuolar protein sorting-associated protein 35 | protein | 744 | 73% helix, 0% strand | G0S709 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 965 | 0.90 | 0.92 | 122 | empty |
| 2 | 1000 | 0.90 | 0.92 | 124 | empty |
| 3 | 1135 | 0.89 | 0.90 | 101 | empty |
| 4 | 1192 | 0.89 | 0.90 | 105 | empty |
| 5 | 1187 | 0.89 | 0.90 | 109 | empty |
Interfaces
30 interfaces between chains.
- O–P · 2687 Ų buried · 13 hydrogen bonds · protein-protein
- M–N · 2680 Ų buried · 13 hydrogen bonds · protein-protein
- B–A · 1515 Ų buried · 15 hydrogen bonds · protein-protein
- H–F · 1515 Ų buried · 15 hydrogen bonds · protein-protein
- G–E · 1512 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 6H7W · Model of retromer-Vps5 complex assembled on membrane. · the same entry in another collection · chain J against J, 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 G0S0E6
- Every structure of UniProt G0SH11
- Every structure of UniProt G0RZB5
- Every structure of UniProt G0S709
- Elsewhere: RCSB PDB 6H7W · PDBe 6H7W · UniProt G0S0E6 · UniProt G0SH11 · UniProt G0RZB5 · UniProt G0S709
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