Research workbench
Cryo-EM structure of 9-fold symmetric ratcpn-beta in ATP-binding state
Analyse Cryo-EM structure of 9-fold symmetric ratcpn-beta in ATP-binding state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3J1F
- Type
- protein
- Length
- 9,090 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chaperonin beta subunit
- UniProt
- Q877H2
- Ligands
- ATP, MG
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 1 distinct chain · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, K, L, M, N, O, P, Q, R, S | Chaperonin beta subunit | protein | 505 | 50% helix, 18% strand | Q877H2 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 18 copies · chains A, B, C, D, E, F, G, H, I, K, L, M, N, O, P, Q, R, S
- MG · Magnesium ion · metal · 18 copies · chains A, B, C, D, E, F, G, H, I, K, L, M, N, O, P, Q, R, S
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 | 976 | 0.81 | 0.82 | 95 | ATP, MG |
| 2 | 998 | 0.80 | 0.81 | 98 | ATP, MG |
| 3 | 817 | 0.80 | 0.83 | 86 | ATP, MG |
| 4 | 992 | 0.80 | 0.81 | 93 | ATP, MG |
| 5 | 1151 | 0.80 | 0.81 | 111 | ATP, MG |
Interfaces
30 interfaces between chains.
- M–N · 821 Ų buried · 18 hydrogen bonds · protein-protein
- N–O · 819 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 814 Ų buried · 13 hydrogen bonds · protein-protein
- L–M · 808 Ų buried · 11 hydrogen bonds · protein-protein
- K–L · 807 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3J1F · Cryo-EM structure of 9-fold symmetric rATcpn-beta in ATP-binding state · the same entry in another collection · chain N against N, 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 Q877H2
- Elsewhere: RCSB PDB 3J1F · PDBe 3J1F · UniProt Q877H2
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