MolNFT v1 · #137743 · protein
Cryo-EM reconstruction of neisseria gonorrhoeae type IV pilus
5VXX · Fimbrial protein: “Cryo-EM reconstruction of neisseria gonorrhoeae type IV pilus”. Electron microscopy, 3 ligands (B6D, OPE, GLA), 20 pockets (best druggability 0.80). MolNFT v1 #137743 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5VXX
- Type
- protein
- Length
- 3,276 residues
- Chains
- 21
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fimbrial protein
- UniProt
- P02974
- Ligands
- B6D, OPE, GLA
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 1 distinct chain · 28% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U | Fimbrial protein | protein | 156 | 28% helix, 21% strand | P02974 |
Ligands and binding sites
- B6D · 2,4-bisacetamido-2,4,6-trideoxy-beta-D-glucopyranose · ligand · 21 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U
- OPE · Phosphoric acid mono-(2-amino-ethyl) ester · ligand · 21 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U
- GLA · alpha-D-galactopyranose · sugar · 21 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 183 | 0.80 | 0.94 | 51 | empty |
| 2 | 135 | 0.77 | 0.95 | 34 | empty |
| 3 | 126 | 0.77 | 0.95 | 27 | empty |
| 4 | 113 | 0.75 | 0.95 | 28 | empty |
| 5 | 113 | 0.75 | 0.94 | 29 | empty |
Interfaces
69 interfaces between chains.
- B–F · 980 Ų buried · 9 hydrogen bonds · protein-protein
- C–G · 979 Ų buried · 9 hydrogen bonds · protein-protein
- O–S · 979 Ų buried · 9 hydrogen bonds · protein-protein
- H–L · 979 Ų buried · 9 hydrogen bonds · protein-protein
- G–K · 978 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 covalent, 21 disulfide (covalent ligand, disulfide).
Compared structures
- 5VXX · Cryo-EM reconstruction of Neisseria gonorrhoeae Type IV pilus · the same entry in another collection · chain M against M, 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 P02974
- Elsewhere: RCSB PDB 5VXX · PDBe 5VXX · UniProt P02974
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