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Crystal structure of thermotoga maritima tmcal bound with alpha-thio ATP(FORM II)
Analyse Crystal structure of thermotoga maritima tmcal bound with alpha-thio ATP(FORM… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y0T
- Type
- protein
- Length
- 1,654 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thermotoga maritima tmcal
- Ligands
- TAT
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 58% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thermotoga maritima tmcal | protein | 414 | 58% helix, 11% strand | — |
| B, D | Thermotoga maritima tmcal | protein | 414 | 58% helix, 11% strand | — |
| C | Thermotoga maritima tmcal | protein | 412 | 59% helix, 11% strand | — |
Ligands and binding sites
- TAT · Adenosine-5'-rp-alpha-thio-triphosphate · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, C, D
- 1PE · Pentaethylene glycol · additive · chains D
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 | 361 | 0.82 | 0.92 | 37 | empty |
| 2 | 851 | 0.77 | 0.80 | 74 | TAT, EDO |
| 3 | 826 | 0.77 | 0.80 | 77 | TAT, 1PE |
| 4 | 832 | 0.76 | 0.80 | 74 | TAT |
| 5 | 719 | 0.74 | 0.79 | 75 | TAT, EDO |
Interfaces
5 interfaces between chains.
- A–B · 1248 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1195 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 1017 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 255 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 254 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified, 4 disulfide (disulfide, artifact, oxidation).
Compared structures
- 5Y0T · Crystal structure of Thermotoga maritima TmcAL bound with alpha-thio ATP(Form II) · 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
- Elsewhere: RCSB PDB 5Y0T · PDBe 5Y0T
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