Research workbench
Structure of an extracellular giant hemoglobin of the gutless beard worm oligobrachia mashikoi
Analyse Structure of an extracellular giant hemoglobin of the gutless beard worm… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D2M
- Type
- protein
- Length
- 573 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Giant hemoglobin, A1(B) globin chain; Giant hemoglobin, A2(A5) globin chain; Giant…
- UniProt
- Q7M419, Q7M413, Q7M418, Q5KSB7
- Ligands
- HEM, OXY
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Giant hemoglobin, A1(B) globin chain | protein | 140 | 72% helix, 0% strand | Q7M419 |
| B | Giant hemoglobin, A2(A5) globin chain | protein | 142 | 75% helix, 0% strand | Q7M413 |
| C | Giant hemoglobin, B2(C) globin chain | protein | 146 | 69% helix, 0% strand | Q7M418 |
| D | Giant hemoglobin, B1(D) globin chain | protein | 145 | 69% helix, 0% strand | Q5KSB7 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, D, B, C
- 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
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 821 | 0.85 | 0.87 | 69 | HEM, OXY |
| 2 | 772 | 0.83 | 0.86 | 72 | HEM, OXY |
| 3 | 929 | 0.78 | 0.80 | 101 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1190 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 808 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 545 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 479 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 164 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 2D2M · Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia… · the same entry in another collection · chain D against D, TM-score 1.00
- Q7M419 · AlphaFold monomer V2.0 prediction for extracellular giant hemoglobin major globin subunit… · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q7M413 · AlphaFold monomer V2.0 prediction for extracellular giant hemoglobin major globin subunit… · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q7M418 · AlphaFold monomer V2.0 prediction for extracellular giant hemoglobin major globin subunit… · a predicted model of the same protein · chain C against A, TM-score 0.97
- Q5KSB7 · AlphaFold monomer V2.0 prediction for extracellular giant hemoglobin major globin subunit… · a predicted model of the same protein · chain D against A, TM-score 0.96
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 Q7M419
- Every structure of UniProt Q7M413
- Every structure of UniProt Q7M418
- Every structure of UniProt Q5KSB7
- Elsewhere: RCSB PDB 2D2M · PDBe 2D2M · UniProt Q7M419 · UniProt Q7M413 · UniProt Q7M418 · UniProt Q5KSB7
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