MolNFT v1 · #167423 · protein
Cryo-EM structure of pila-N/C from geobacter sulfurreducens
6VK9 · Geopilin domain 1 protein: “Cryo-EM structure of pila-N/C from geobacter sulfurreducens”. Electron microscopy, 20 pockets (best druggability 0.81). MolNFT v1 #167423 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6VK9
- Type
- protein
- Length
- 2,640 residues
- Chains
- 32
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Geopilin domain 1 protein; Geopilin domain 2 protein
- UniProt
- Q74D23, Q74D22
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 2 distinct chains · 23% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, O, Q, S, U, G, I, K, M, C, E, W, Y, 0, 2, 4 | Geopilin domain 1 protein | protein | 61 | 62% helix, 0% strand | Q74D23 |
| D, B, P, R, T, V, H, J, L, N, F, X, Z, 1, 3, 5 | Geopilin domain 2 protein | protein | 104 | 0% helix, 24% strand | Q74D22 |
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1181 | 0.81 | 0.83 | 113 | empty |
| 2 | 665 | 0.77 | 0.83 | 68 | empty |
| 3 | 633 | 0.77 | 0.83 | 59 | empty |
| 4 | 603 | 0.76 | 0.83 | 58 | empty |
| 5 | 638 | 0.76 | 0.82 | 65 | empty |
Interfaces
166 interfaces between chains.
- A–B · 1542 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 1534 Ų buried · 23 hydrogen bonds · protein-protein
- O–P · 1531 Ų buried · 23 hydrogen bonds · protein-protein
- Y–Z · 1530 Ų buried · 23 hydrogen bonds · protein-protein
- M–N · 1530 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 6VK9 · Cryo-EM structure of PilA-N/C from Geobacter sulfurreducens · the same entry in another collection · chain O against O, 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 Q74D23
- Every structure of UniProt Q74D22
- Elsewhere: RCSB PDB 6VK9 · PDBe 6VK9 · UniProt Q74D23 · UniProt Q74D22
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