MolNFT v1 · #40056 · protein
Crystal structure of uncharacterized conserved archael protein from methanopyrus kandleri
2IEC · Uncharacterized protein conserved in archaea: “Crystal structure of uncharacterized conserved archael protein from methanopyrus kandleri”. X-ray diffraction, 1 ligand (MG), 2 pockets (best druggability 0.76). MolNFT v1 #40056 on…
- PDB
- 2IEC
- Type
- protein
- Length
- 455 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein conserved in archaea
- UniProt
- Q8TX89
- Ligands
- MG
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein conserved in archaea | protein | 113 | 37% helix, 37% strand | Q8TX89 |
| B | Uncharacterized protein conserved in archaea | protein | 114 | 30% helix, 36% strand | Q8TX89 |
| C | Uncharacterized protein conserved in archaea | protein | 111 | 29% helix, 38% strand | Q8TX89 |
| D | Uncharacterized protein conserved in archaea | protein | 117 | 33% helix, 36% strand | Q8TX89 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains B, C, D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 556 | 0.76 | 0.83 | 65 | empty |
| 2 | 563 | 0.74 | 0.81 | 65 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1265 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1007 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 953 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 942 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 635 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 2IEC · Crystal Structure of uncharacterized conserved archael protein from Methanopyrus kandleri · the same entry in another collection · chain D against D, TM-score 1.00
- Q8TX89 · AlphaFold monomer V2.0 prediction for dihydroneopterin aldolase (Q8TX89) · a predicted model of the same protein · 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 Q8TX89
- Elsewhere: RCSB PDB 2IEC · PDBe 2IEC · UniProt Q8TX89
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