Research workbench
Agme bound to ADP-B-mannose
Analyse Agme bound to ADP-B-mannose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X86
- Type
- protein
- Length
- 6,140 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-L-glycero-D-manno-heptose-6-epimerase
- EC
- 5.1.3.20
- UniProt
- P67911
- Ligands
- NAP, ADP, BMA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T | ADP-L-glycero-D-manno-heptose-6-epimerase (EC 5.1.3.20) | protein | 307 | 46% helix, 17% strand | P67911 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 20 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
- ADP · Adenosine-5'-diphosphate · ligand · 20 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
- BMA · beta-D-mannopyranose · sugar · 19 copies · chains A, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 783 | 0.83 | 0.86 | 74 | NAP, ADP, BMA |
| 2 | 779 | 0.83 | 0.86 | 71 | NAP, ADP, BMA |
| 3 | 786 | 0.83 | 0.86 | 76 | NAP, ADP, BMA |
| 4 | 783 | 0.83 | 0.86 | 71 | NAP, ADP, BMA |
| 5 | 802 | 0.83 | 0.86 | 72 | NAP, ADP, BMA |
Interfaces
33 interfaces between chains.
- L–M · 829 Ų buried · 15 hydrogen bonds · protein-protein
- Q–R · 828 Ų buried · 14 hydrogen bonds · protein-protein
- F–J · 826 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 826 Ų buried · 14 hydrogen bonds · protein-protein
- H–I · 826 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 2X86 · AGME bound to ADP-B-mannose · the same entry in another collection · chain T against T, 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 P67911
- Elsewhere: RCSB PDB 2X86 · PDBe 2X86 · UniProt P67911
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