Research workbench
Crystal structure determination of lepus europaeus 2.8 a resolution
Analyse Crystal structure determination of lepus europaeus 2.8 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LQD
- Type
- protein
- Length
- 574 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha; Hemoglobin subunit beta
- UniProt
- P08535
- Ligands
- HEM, OXY
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin subunit alpha | protein | 141 | 74% helix, 0% strand | — |
| B, D | Hemoglobin subunit beta | protein | 146 | 79% helix, 0% strand | P08535 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- OXY · Oxygen molecule · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 711 | 0.83 | 0.87 | 91 | empty |
| 2 | 465 | 0.78 | 0.86 | 52 | empty |
| 3 | 221 | 0.75 | 0.89 | 28 | HEM, OXY |
| 4 | 195 | 0.72 | 0.88 | 24 | HEM, OXY |
| 5 | 226 | 0.71 | 0.86 | 30 | HEM, OXY |
Interfaces
6 interfaces between chains.
- C–D · 948 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 943 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 523 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 514 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 393 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3LQD · Crystal structure determination of Lepus europaeus 2.8 A resolution · the same entry in another collection · chain A against A, TM-score 1.00
- P08535 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta (P08535) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P08535
- Elsewhere: RCSB PDB 3LQD · PDBe 3LQD · UniProt P08535
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