MolNFT v1 · #79251 · protein
Crystal structure of helicobacter pylori ADP-L-glycero-D-manno- heptose-6-epimerase (rfad, HP0859)
3SXP · ADP-L-glycero-D-mannoheptose-6-epimerase: “Crystal structure of helicobacter pylori ADP-L-glycero-D-manno- heptose-6-epimerase (rfad, HP0859)”. X-ray diffraction, 1 ligand (NAD), 20 pockets (best druggability 0.79). MolNFT v1 #79251…
- PDB
- 3SXP
- Type
- protein
- Length
- 1,555 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-L-glycero-D-mannoheptose-6-epimerase
- EC
- 5.1.3.20
- UniProt
- B5Z7L9
- Ligands
- NAD
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | ADP-L-glycero-D-mannoheptose-6-epimerase (EC 5.1.3.20) | protein | 310 | 41% helix, 18% strand | B5Z7L9 |
| B | ADP-L-glycero-D-mannoheptose-6-epimerase (EC 5.1.3.20) | protein | 311 | 41% helix, 17% strand | B5Z7L9 |
| D | ADP-L-glycero-D-mannoheptose-6-epimerase (EC 5.1.3.20) | protein | 314 | 41% helix, 17% strand | B5Z7L9 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 912 | 0.79 | 0.81 | 76 | NAD |
| 2 | 812 | 0.79 | 0.82 | 71 | NAD |
| 3 | 746 | 0.78 | 0.83 | 65 | NAD |
| 4 | 805 | 0.78 | 0.82 | 65 | NAD |
| 5 | 807 | 0.78 | 0.82 | 68 | NAD |
Interfaces
5 interfaces between chains.
- A–D · 955 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 955 Ų buried · 12 hydrogen bonds · protein-protein
- C–E · 949 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 946 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 944 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3SXP · Crystal Structure of Helicobacter pylori ADP-L-glycero-D-manno-heptose-6-epimerase (rfaD… · 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 B5Z7L9
- Elsewhere: RCSB PDB 3SXP · PDBe 3SXP · UniProt B5Z7L9
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