Research workbench
Crystal structure of peroxisomal catalase from the yeast hansenula polymorpha
Analyse Crystal structure of peroxisomal catalase from the yeast hansenula polymorpha in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XQ1
- Type
- protein
- Length
- 7,860 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisomal catalase
- EC
- 1.11.1.6
- UniProt
- P30263
- Ligands
- HEM
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 12 distinct chains · 32% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, I | Peroxisomal catalase (EC 1.11.1.6) | protein | 491 | 32% helix, 19% strand | P30263 |
| B, D, F | Peroxisomal catalase (EC 1.11.1.6) | protein | 494 | 32% helix, 19% strand | P30263 |
| C | Peroxisomal catalase (EC 1.11.1.6) | protein | 492 | 32% helix, 19% strand | P30263 |
| E | Peroxisomal catalase (EC 1.11.1.6) | protein | 490 | 32% helix, 19% strand | P30263 |
| G, P | Peroxisomal catalase (EC 1.11.1.6) | protein | 491 | 32% helix, 19% strand | P30263 |
| H | Peroxisomal catalase (EC 1.11.1.6) | protein | 487 | 33% helix, 19% strand | P30263 |
| J | Peroxisomal catalase (EC 1.11.1.6) | protein | 491 | 33% helix, 19% strand | P30263 |
| K | Peroxisomal catalase (EC 1.11.1.6) | protein | 490 | 33% helix, 19% strand | P30263 |
| L | Peroxisomal catalase (EC 1.11.1.6) | protein | 489 | 33% helix, 19% strand | P30263 |
| M | Peroxisomal catalase (EC 1.11.1.6) | protein | 491 | 32% helix, 19% strand | P30263 |
| N | Peroxisomal catalase (EC 1.11.1.6) | protein | 491 | 32% helix, 19% strand | P30263 |
| O | Peroxisomal catalase (EC 1.11.1.6) | protein | 493 | 31% helix, 19% strand | P30263 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 15 copies · chains B, C, A, D, E, H, F, G, I, L, J, K, M, P, N, O
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 | 699 | 0.88 | 0.92 | 52 | empty |
| 2 | 716 | 0.88 | 0.92 | 52 | empty |
| 3 | 708 | 0.87 | 0.91 | 53 | empty |
| 4 | 709 | 0.87 | 0.91 | 55 | empty |
| 5 | 273 | 0.85 | 0.96 | 40 | empty |
Interfaces
37 interfaces between chains.
- J–K · 4988 Ų buried · 52 hydrogen bonds · protein-protein
- M–P · 4982 Ų buried · 52 hydrogen bonds · protein-protein
- N–O · 4981 Ų buried · 49 hydrogen bonds · protein-protein
- B–C · 4968 Ų buried · 50 hydrogen bonds · protein-protein
- F–G · 4965 Ų buried · 51 hydrogen bonds · protein-protein
Compared structures
- 2XQ1 · Crystal structure of peroxisomal catalase from the yeast Hansenula polymorpha · the same entry in another collection · chain K against K, 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 P30263
- Elsewhere: RCSB PDB 2XQ1 · PDBe 2XQ1 · UniProt P30263
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