Research workbench
1.70 ångström resolution crystal structure of outer-membrane lipoprotein carrier protein (lola) from yersinia pestis CO92
Analyse 1.70 ångström resolution crystal structure of outer-membrane lipoprotein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KI3
- Type
- protein
- Length
- 2,103 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer-membrane lipoprotein carrier protein
- UniProt
- E8P443
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 9 distinct chains · 16% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, F, J | Outer-membrane lipoprotein carrier protein | protein | 177 | 16% helix, 50% strand | E8P443 |
| B | Outer-membrane lipoprotein carrier protein | protein | 169 | 16% helix, 50% strand | E8P443 |
| D | Outer-membrane lipoprotein carrier protein | protein | 179 | 16% helix, 51% strand | E8P443 |
| E | Outer-membrane lipoprotein carrier protein | protein | 169 | 16% helix, 50% strand | E8P443 |
| G | Outer-membrane lipoprotein carrier protein | protein | 179 | 15% helix, 50% strand | E8P443 |
| H | Outer-membrane lipoprotein carrier protein | protein | 172 | 15% helix, 51% strand | E8P443 |
| I | Outer-membrane lipoprotein carrier protein | protein | 180 | 15% helix, 51% strand | E8P443 |
| K | Outer-membrane lipoprotein carrier protein | protein | 171 | 16% helix, 50% strand | E8P443 |
| L | Outer-membrane lipoprotein carrier protein | protein | 176 | 15% helix, 50% strand | E8P443 |
Ligands and binding sites
- ACT · Acetate ion · additive · 7 copies · chains A, B, D, F, G, H, I
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, D, J, L
- GOL · Glycerol · additive · 2 copies · chains A, B, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 762 | 0.82 | 0.85 | 93 | empty |
| 2 | 641 | 0.80 | 0.85 | 72 | empty |
| 3 | 733 | 0.79 | 0.84 | 92 | ACT |
| 4 | 824 | 0.79 | 0.82 | 107 | empty |
| 5 | 756 | 0.78 | 0.82 | 84 | ACT |
Interfaces
21 interfaces between chains.
- H–I · 994 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 975 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 953 Ų buried · 9 hydrogen bonds · protein-protein
- C–E · 948 Ų buried · 7 hydrogen bonds · protein-protein
- G–I · 946 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4KI3 · 1.70 Angstrom resolution crystal structure of outer-membrane lipoprotein carrier protein… · the same entry in another collection · chain A against A, 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 E8P443
- Elsewhere: RCSB PDB 4KI3 · PDBe 4KI3 · UniProt E8P443
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