Research workbench
Structure of the cobalt-bound form of the deoxy-D-mannose-octulosonate 8-phosphate phosphatase (yrbi) from haemophilus influenzae (HI1679)
Analyse Structure of the cobalt-bound form of the deoxy-D-mannose-octulosonate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1K1E
- Type
- protein
- Length
- 2,090 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxy-D-mannose-octulosonate 8-phosphate phosphatase
- EC
- 3.1.3.-
- UniProt
- P45314
- Ligands
- CO, HG, SO4
- Pockets
- 19 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F, I, J | Deoxy-D-mannose-octulosonate 8-phosphate phosphatase (EC 3.1.3.-) | protein | 177 | 45% helix, 22% strand | P45314 |
| C | Deoxy-D-mannose-octulosonate 8-phosphate phosphatase (EC 3.1.3.-) | protein | 174 | 43% helix, 22% strand | P45314 |
| D | Deoxy-D-mannose-octulosonate 8-phosphate phosphatase (EC 3.1.3.-) | protein | 170 | 41% helix, 23% strand | P45314 |
| G, L | Deoxy-D-mannose-octulosonate 8-phosphate phosphatase (EC 3.1.3.-) | protein | 170 | 43% helix, 22% strand | P45314 |
| H | Deoxy-D-mannose-octulosonate 8-phosphate phosphatase (EC 3.1.3.-) | protein | 171 | 43% helix, 23% strand | P45314 |
| K | Deoxy-D-mannose-octulosonate 8-phosphate phosphatase (EC 3.1.3.-) | protein | 173 | 43% helix, 22% strand | P45314 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- HG · Mercury (II) ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- SO4 · Sulfate ion · ion · 18 copies · chains A, B, D, C, E, F, H, G, I, J, L, K
- GOL · Glycerol · additive · 6 copies · chains A, C, G, I, K
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 3 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 797 | 0.82 | 0.85 | 70 | empty |
| 2 | 991 | 0.82 | 0.83 | 79 | empty |
| 3 | 881 | 0.81 | 0.83 | 70 | empty |
| 4 | 871 | 0.80 | 0.83 | 72 | empty |
| 5 | 100 | 0.74 | 0.95 | 20 | CO, SO4 |
Interfaces
21 interfaces between chains.
- I–K · 1178 Ų buried · 22 hydrogen bonds · protein-protein
- E–G · 1175 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1160 Ų buried · 24 hydrogen bonds · protein-protein
- I–J · 1152 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 1152 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 1K1E · Structure Of the cobalt-bound form of the deoxy-D-mannose-octulosonate 8-phosphate… · 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 P45314
- Elsewhere: RCSB PDB 1K1E · PDBe 1K1E · UniProt P45314
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