MolNFT v1 · #141616 · protein
Cryoem structure of etec pilotin-secretin asps-gspd complex
5ZDH · Type II secretion system protein D: “Cryoem structure of etec pilotin-secretin asps-gspd complex”. Electron microscopy, 20 pockets (best druggability 0.81). MolNFT v1 #141616 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5ZDH
- Type
- protein
- Length
- 8,715 residues
- Chains
- 30
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type II secretion system protein D; Type II secretion system lipoprotein
- UniProt
- E3PJ86, E3PJ88
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 2 distinct chains · 26% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O | Type II secretion system protein D | protein | 497 | 25% helix, 36% strand | E3PJ86 |
| P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d | Type II secretion system lipoprotein | protein | 84 | 32% helix, 21% strand | E3PJ88 |
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 | 977 | 0.81 | 0.83 | 104 | empty |
| 2 | 947 | 0.81 | 0.83 | 93 | empty |
| 3 | 973 | 0.81 | 0.82 | 97 | empty |
| 4 | 945 | 0.81 | 0.83 | 98 | empty |
| 5 | 893 | 0.81 | 0.83 | 100 | empty |
Interfaces
75 interfaces between chains.
- E–F · 5691 Ų buried · 70 hydrogen bonds · protein-protein
- M–N · 5688 Ų buried · 70 hydrogen bonds · protein-protein
- A–O · 5684 Ų buried · 70 hydrogen bonds · protein-protein
- H–I · 5679 Ų buried · 70 hydrogen bonds · protein-protein
- K–L · 5678 Ų buried · 70 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 5ZDH · CryoEM structure of ETEC Pilotin-Secretin AspS-GspD complex · the same entry in another collection · chain K against K, 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 E3PJ86
- Every structure of UniProt E3PJ88
- Elsewhere: RCSB PDB 5ZDH · PDBe 5ZDH · UniProt E3PJ86 · UniProt E3PJ88
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