MolNFT v1 · #181650 · protein
X-ray structure of CJ1430 in the presence of GDP, a GDP-D-glycero-4- keto-D-lyxo-heptose-3,5-epimerase from campylobacter jejuni
7M14 · Thymidine diphospho-4-keto-rhamnose 3,5-epimerase: “X-ray structure of CJ1430 in the presence of GDP, a GDP-D-glycero-4- keto-D-lyxo-heptose-3,5-epimerase from…”. X-ray diffraction, 2 ligands (GDP, NA), 12 pockets (best druggability…
- PDB
- 7M14
- Type
- protein
- Length
- 1,064 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidine diphospho-4-keto-rhamnose 3,5-epimerase
- EC
- 5.1.3.13
- UniProt
- Q0P8I4
- Ligands
- GDP, NA
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidine diphospho-4-keto-rhamnose 3,5-epimerase (EC 5.1.3.13) | protein | 178 | 10% helix, 47% strand | Q0P8I4 |
| B, C | Thymidine diphospho-4-keto-rhamnose 3,5-epimerase (EC 5.1.3.13) | protein | 179 | 10% helix, 47% strand | Q0P8I4 |
| D, E | Thymidine diphospho-4-keto-rhamnose 3,5-epimerase (EC 5.1.3.13) | protein | 177 | 8% helix, 49% strand | Q0P8I4 |
| F | Thymidine diphospho-4-keto-rhamnose 3,5-epimerase (EC 5.1.3.13) | protein | 174 | 6% helix, 48% strand | Q0P8I4 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- NA · Sodium ion · metal · chains B
- EDO · 1,2-ethanediol · additive · 2 copies · chains C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1118 | 0.77 | 0.79 | 113 | empty |
| 2 | 244 | 0.72 | 0.87 | 34 | GDP |
| 3 | 520 | 0.72 | 0.81 | 67 | GDP |
| 4 | 317 | 0.72 | 0.85 | 43 | GDP |
| 5 | 321 | 0.71 | 0.84 | 42 | GDP |
Interfaces
10 interfaces between chains.
- C–D · 1685 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 1675 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1628 Ų buried · 36 hydrogen bonds · protein-protein
- A–E · 807 Ų buried · 24 hydrogen bonds · protein-protein
- D–E · 458 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7M14 · x-ray structure of cj1430 in the presence of GDP, a… · 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 Q0P8I4
- Elsewhere: RCSB PDB 7M14 · PDBe 7M14 · UniProt Q0P8I4
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