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Crystal structure of a guanylate kinase from stenotrophomonas maltophilia K279A with heterogeneous ligand states of GMP/ADP, gmp/-, GDP/-, and GMP/ATPGS
Analyse Crystal structure of a guanylate kinase from stenotrophomonas maltophilia K279A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S5E
- Type
- protein
- Length
- 1,612 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanylate kinase
- EC
- 2.7.4.8
- UniProt
- B2FT06
- Ligands
- 5GP, ADP, GDP, AGS
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Guanylate kinase (EC 2.7.4.8) | protein | 203 | 48% helix, 21% strand | B2FT06 |
| B, F | Guanylate kinase (EC 2.7.4.8) | protein | 198 | 47% helix, 21% strand | B2FT06 |
| C, G | Guanylate kinase (EC 2.7.4.8) | protein | 198 | 47% helix, 21% strand | B2FT06 |
| D, H | Guanylate kinase (EC 2.7.4.8) | protein | 207 | 48% helix, 20% strand | B2FT06 |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · 6 copies · chains A, B, D, E, F, H
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, E
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains C, G
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 2 copies · chains D, 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1070 | 0.80 | 0.82 | 117 | empty |
| 2 | 446 | 0.70 | 0.81 | 46 | 5GP, ADP |
| 3 | 411 | 0.69 | 0.81 | 44 | 5GP, ADP |
| 4 | 662 | 0.66 | 0.76 | 64 | 5GP, AGS |
| 5 | 536 | 0.63 | 0.76 | 52 | 5GP, AGS |
Interfaces
11 interfaces between chains.
- A–C · 1585 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1556 Ų buried · 11 hydrogen bonds · protein-protein
- F–H · 1555 Ų buried · 11 hydrogen bonds · protein-protein
- E–G · 1552 Ų buried · 12 hydrogen bonds · protein-protein
- D–G · 686 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7S5E · Crystal structure of a guanylate kinase from Stenotrophomonas maltophilia K279a with… · 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 B2FT06
- Elsewhere: RCSB PDB 7S5E · PDBe 7S5E · UniProt B2FT06
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