MolNFT v1 · #140126 · protein
Crystal structure of apo thermotoga maritima TMCAL(FORM II)
5Y0S: “Crystal structure of apo thermotoga maritima TMCAL(FORM II)”. X-ray diffraction, 20 pockets (best druggability 0.83). MolNFT v1 #140126 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5Y0S
- Type
- protein
- Length
- 1,692 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thermotoga maritima tmcal
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 56% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Thermotoga maritima tmcal | protein | 423 | 56% helix, 11% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 22 copies · chains A, C, B, 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 363 | 0.83 | 0.93 | 38 | EDO |
| 2 | 976 | 0.81 | 0.82 | 84 | empty |
| 3 | 951 | 0.81 | 0.82 | 78 | empty |
| 4 | 976 | 0.79 | 0.81 | 75 | empty |
| 5 | 760 | 0.77 | 0.81 | 76 | EDO |
Interfaces
5 interfaces between chains.
- A–B · 1240 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1194 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1038 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 257 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 254 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified, 4 disulfide (disulfide, artifact, oxidation).
Compared structures
- 5Y0S · Crystal structure of apo Thermotoga maritima TmcAL(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 5Y0S · PDBe 5Y0S
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