MolNFT v1 · #34020 · protein
Structure of an extracellular giant hemoglobin of the gutless beard worm oligobrachia mashikoi
2D2N · Giant hemoglobin, A1(B) globin chain: “Structure of an extracellular giant hemoglobin of the gutless beard worm oligobrachia mashikoi”. X-ray diffraction, 3 ligands (HEM, MMC, OXY), 5 pockets (best druggability 0.85). MolNFT v1…
- PDB
- 2D2N
- 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, MMC, OXY
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Giant hemoglobin, A1(B) globin chain | protein | 140 | 74% 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 | 71% helix, 0% strand | Q7M418 |
| D | Giant hemoglobin, B1(D) globin chain | protein | 145 | 71% helix, 0% strand | Q5KSB7 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, D, B, C
- MMC · Methyl mercury ion · 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
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 829 | 0.85 | 0.87 | 68 | HEM, OXY, MMC |
| 2 | 825 | 0.83 | 0.85 | 71 | HEM, OXY |
| 3 | 508 | 0.70 | 0.80 | 57 | empty |
| 4 | 239 | 0.57 | 0.79 | 34 | empty |
| 5 | 94 | 0.41 | 0.78 | 24 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1212 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 851 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 538 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 470 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 167 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 2D2N · 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 2D2N · PDBe 2D2N · UniProt Q7M419 · UniProt Q7M413 · UniProt Q7M418 · UniProt Q5KSB7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.