Research workbench
Human centrin 2 xeroderma pigmentosum group C protein complex
Analyse Human centrin 2 xeroderma pigmentosum group C protein complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GGM
- Type
- protein
- Length
- 327 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Centrin-2; DNA-repair protein complementing xp-C cells
- UniProt
- P41208, Q01831
- Ligands
- CA
- Pockets
- 5 · best druggability 0.45
Structure
x-ray diffraction · 3 distinct chains · 64% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Centrin-2 | protein | 149 | 61% helix, 5% strand | P41208 |
| B | Centrin-2 | protein | 144 | 63% helix, 6% strand | P41208 |
| C, D | DNA-repair protein complementing xp-C cells | protein | 17 | 88% helix, 0% strand | Q01831 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.45 | 0.77 | 20 | empty |
| 2 | 161 | 0.45 | 0.75 | 18 | empty |
| 3 | 140 | 0.45 | 0.76 | 23 | empty |
| 4 | 63 | 0.42 | 0.81 | 12 | empty |
| 5 | 64 | 0.32 | 0.75 | 11 | empty |
Interfaces
6 interfaces between chains.
- A–C · 877 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 812 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 308 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 168 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 105 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 2GGM · Human centrin 2 xeroderma pigmentosum group C protein complex · the same entry in another collection · chain A against A, TM-score 1.00
- P41208 · AlphaFold monomer V2.0 prediction for centrin-2 (P41208) · a predicted model of the same protein · chain B against A, TM-score 0.91
- Q01831 · AlphaFold monomer V2.0 prediction for DNA repair protein complementing xp-C cells (Q01831) · a predicted model of the same protein · chain C against A, TM-score 0.74
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 P41208
- Every structure of UniProt Q01831
- Elsewhere: RCSB PDB 2GGM · PDBe 2GGM · UniProt P41208 · UniProt Q01831
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