MolNFT v1 · #34019 · protein
Structure of an extracellular giant hemoglobin of the gutless beard worm oligobrachia mashikoi
2D2M · Giant hemoglobin, A1(B) globin chain: “Structure of an extracellular giant hemoglobin of the gutless beard worm oligobrachia mashikoi”. X-ray diffraction, 2 ligands (HEM, OXY), 3 pockets (best druggability 0.85). MolNFT v1 #34019 on…
- 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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