MolNFT v1 · #154579 · protein
Groel from xanthomonas oryzae pv. oryzae
6KFV · 60 kda chaperonin: “Groel from xanthomonas oryzae pv. oryzae”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.79). MolNFT v1 #154579 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6KFV
- Type
- protein
- Length
- 7,342 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 60 kda chaperonin
- UniProt
- A0A0U2JHN9
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, L, M | 60 kda chaperonin | protein | 525 | 51% helix, 17% strand | A0A0U2JHN9 |
| K | 60 kda chaperonin | protein | 518 | 47% helix, 16% strand | A0A0U2JHN9 |
| N | 60 kda chaperonin | protein | 524 | 49% helix, 13% strand | A0A0U2JHN9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains G, I, E, K
- GOL · Glycerol · additive · 3 copies · chains B, F
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 | 861 | 0.79 | 0.82 | 93 | empty |
| 2 | 1046 | 0.79 | 0.81 | 97 | empty |
| 3 | 1172 | 0.78 | 0.80 | 116 | empty |
| 4 | 844 | 0.78 | 0.82 | 73 | empty |
| 5 | 1048 | 0.78 | 0.80 | 96 | empty |
Interfaces
28 interfaces between chains.
- A–N · 1870 Ų buried · 22 hydrogen bonds · protein-protein
- I–M · 1770 Ų buried · 21 hydrogen bonds · protein-protein
- B–M · 1753 Ų buried · 14 hydrogen bonds · protein-protein
- G–I · 1729 Ų buried · 17 hydrogen bonds · protein-protein
- C–J · 1729 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6KFV · GroEL from Xanthomonas oryzae pv. oryzae · the same entry in another collection · chain C against C, 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 A0A0U2JHN9
- Elsewhere: RCSB PDB 6KFV · PDBe 6KFV · UniProt A0A0U2JHN9
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