MolNFT v1 · #163345 · protein
C-terminally extended and N-terminally truncated variant of fima E. COLI at 1.5 ångström resolution
6S09: “C-terminally extended and N-terminally truncated variant of fima E. COLI at 1.5 ångström resolution”. X-ray diffraction, 2 ligands (NA, SO4), 12 pockets (best druggability 0.78). MolNFT v1 #163345 on GenesisL1: 3D structure, binding…
- PDB
- 6S09
- Type
- protein
- Length
- 1,300 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fima
- UniProt
- M4YRT1
- Ligands
- NA, SO4
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 8 distinct chains · 4% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | Fima | protein | 166 | 6% helix, 55% strand | M4YRT1 |
| A | Fima | protein | 161 | 5% helix, 53% strand | M4YRT1 |
| B | Fima | protein | 156 | 2% helix, 56% strand | M4YRT1 |
| C | Fima | protein | 164 | 4% helix, 54% strand | M4YRT1 |
| D | Fima | protein | 161 | 4% helix, 52% strand | M4YRT1 |
| E | Fima | protein | 164 | 2% helix, 48% strand | M4YRT1 |
| G | Fima | protein | 163 | 4% helix, 52% strand | M4YRT1 |
| H | Fima | protein | 165 | 2% helix, 45% strand | M4YRT1 |
Ligands and binding sites
- NA · Sodium ion · metal · chains C, H
- SO4 · Sulfate ion · ion · 5 copies · chains F, A, E, B, C, G, H
- ACY · Acetic acid · additive · chains C, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 852 | 0.78 | 0.82 | 125 | empty |
| 2 | 510 | 0.66 | 0.78 | 46 | empty |
| 3 | 354 | 0.62 | 0.78 | 40 | empty |
| 4 | 227 | 0.51 | 0.76 | 40 | empty |
| 5 | 207 | 0.49 | 0.76 | 32 | empty |
Interfaces
14 interfaces between chains.
- B–E · 627 Ų buried · 9 hydrogen bonds · protein-protein
- F–B · 569 Ų buried · 19 hydrogen bonds · protein-protein
- F–E · 478 Ų buried · 10 hydrogen bonds · protein-protein
- C–H · 476 Ų buried · 10 hydrogen bonds · protein-protein
- A–G · 471 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6S09 · C-terminally extended and N-terminally truncated variant of FimA E. coli at 1.5 Angstrom… · the same entry in another collection · chain E against E, 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 M4YRT1
- Elsewhere: RCSB PDB 6S09 · PDBe 6S09 · UniProt M4YRT1
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