Research workbench
Crystal structure of PH1257 from pyrococcus horikoshii OT3
Analyse Crystal structure of PH1257 from pyrococcus horikoshii OT3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D13
- Type
- protein
- Length
- 833 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein PH1257
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein PH1257 | protein | 215 | 34% helix, 30% strand | — |
| B | Hypothetical protein PH1257 | protein | 206 | 33% helix, 32% strand | — |
| C | Hypothetical protein PH1257 | protein | 209 | 34% helix, 31% strand | — |
| D | Hypothetical protein PH1257 | protein | 203 | 34% helix, 32% strand | — |
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 476 | 0.69 | 0.80 | 42 | empty |
| 2 | 396 | 0.64 | 0.78 | 40 | empty |
| 3 | 522 | 0.63 | 0.76 | 64 | empty |
| 4 | 285 | 0.59 | 0.78 | 40 | empty |
| 5 | 414 | 0.59 | 0.75 | 46 | empty |
Interfaces
6 interfaces between chains.
- A–C · 971 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 924 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 214 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 191 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 54 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2D13 · Crystal Structure of PH1257 from Pyrococcus horikoshii OT3 · 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 2D13 · PDBe 2D13
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