Research workbench
Structure of protoglobin from methanosarcina acetivorans C2A
Analyse Structure of protoglobin from methanosarcina acetivorans C2A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VEE
- Type
- protein
- Length
- 1,520 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protoglobin
- UniProt
- Q8TLY9
- Ligands
- HEM
- Pockets
- 15 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 64% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Protoglobin | protein | 190 | 64% helix, 2% strand | Q8TLY9 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 355 | 0.86 | 0.95 | 39 | HEM |
| 2 | 348 | 0.86 | 0.95 | 44 | HEM |
| 3 | 355 | 0.86 | 0.95 | 40 | HEM |
| 4 | 335 | 0.86 | 0.95 | 37 | HEM |
| 5 | 334 | 0.86 | 0.95 | 39 | HEM |
Interfaces
12 interfaces between chains.
- G–H · 1956 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1949 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 1947 Ų buried · 28 hydrogen bonds · protein-protein
- E–F · 1942 Ų buried · 28 hydrogen bonds · protein-protein
- F–H · 452 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2VEE · Structure of protoglobin from Methanosarcina acetivorans C2A · 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
- Every structure of UniProt Q8TLY9
- Elsewhere: RCSB PDB 2VEE · PDBe 2VEE · UniProt Q8TLY9
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