Research workbench
Single-particle cryo-EM using alignment by classification (ABC): the structure of lumbricus terrestris hemoglobin
Analyse Single-particle cryo-EM using alignment by classification (ABC): the structure… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M3L
- Type
- protein
- Length
- 2,394 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Extracellular globin-4; Extracellular globin-2; Extracellular globin-3; Hemoglobin chain…
- UniProt
- P13579, P02218, P11069, O61233, Q9GV76, Q2I743, Q2I742
- Ligands
- HEM
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 8 distinct chains · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I | Extracellular globin-4 | protein | 147 | 61% helix, 0% strand | P13579 |
| B, F | Extracellular globin-2 | protein | 145 | 73% helix, 0% strand | P02218 |
| C, G, K | Extracellular globin-3 | protein | 149 | 70% helix, 0% strand | P11069 |
| D, H, L | Hemoglobin chain D1 | protein | 140 | 77% helix, 0% strand | O61233 |
| J | Extracellular globin-2 | protein | 144 | 74% helix, 0% strand | P02218 |
| M | Hemoglobin linker chain L1 | protein | 217 | 24% helix, 28% strand | Q9GV76 |
| N | Extracellular hemoglobin linker L2 subunit | protein | 220 | 20% helix, 26% strand | Q2I743 |
| O | Extracellular hemoglobin linker L3 subunit | protein | 215 | 23% helix, 29% strand | Q2I742 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 12 copies · chains A, D, B, C, E, H, F, G, I, L, J, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.86 | 0.87 | 90 | HEM |
| 2 | 1025 | 0.86 | 0.86 | 76 | HEM |
| 3 | 1019 | 0.85 | 0.86 | 72 | HEM |
| 4 | 1077 | 0.85 | 0.85 | 79 | HEM |
| 5 | 1094 | 0.85 | 0.85 | 79 | HEM |
Interfaces
37 interfaces between chains.
- M–N · 1313 Ų buried · 4 hydrogen bonds · protein-protein
- N–O · 1265 Ų buried · 6 hydrogen bonds · protein-protein
- M–O · 1169 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 1160 Ų buried · 15 hydrogen bonds · protein-protein
- I–L · 1151 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5M3L · Single-particle cryo-EM using alignment by classification (ABC): the structure of… · the same entry in another collection · chain O against O, 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 P13579
- Every structure of UniProt P02218
- Every structure of UniProt P11069
- Every structure of UniProt O61233
- Every structure of UniProt Q9GV76
- Every structure of UniProt Q2I743
- Every structure of UniProt Q2I742
- Elsewhere: RCSB PDB 5M3L · PDBe 5M3L · UniProt P13579 · UniProt P02218 · UniProt P11069 · UniProt O61233 · UniProt Q9GV76 · UniProt Q2I743 · UniProt Q2I742
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