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The crystallographic structure of the giant hemoglobin from glossoscolex paulistus at 3.2 a resolution.
Analyse The crystallographic structure of the giant hemoglobin from glossoscolex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4U8U
- Type
- protein
- Length
- 7,200 residues
- Chains
- 45
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Globin a chain; Globin B chain; Globin C chain; Globin D chain; Linker L1; Linker L2…
- Ligands
- HEM, NAG, CA, ZN, CYN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 7 distinct chains · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I, P, T, X, e, i, m | Globin a chain | protein | 148 | 73% helix, 0% strand | — |
| B, F, J, Q, U, Y, f, j, n | Globin B chain | protein | 142 | 77% helix, 0% strand | — |
| C, G, K, R, V, Z, g, k, o | Globin C chain | protein | 151 | 76% helix, 0% strand | — |
| D, H, L, S, W, a, h, l, p | Globin D chain | protein | 141 | 77% helix, 0% strand | — |
| M, b, q | Linker L1 | protein | 222 | 25% helix, 32% strand | — |
| N, c, r | Linker L2 | protein | 219 | 23% helix, 34% strand | — |
| O, d, s | Linker L3 | protein | 213 | 23% helix, 39% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 36 copies · chains A, D, B, C, E, H, F, G, I, L, J, K, P, S, Q, R, T, W, U, V, X, a, Y, Z, e, h, f, g, i, l, j, k, m, p, n, o
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains O, d, s
- CA · Calcium ion · metal · 9 copies · chains B, M, N, J, O, Q, b, c, Y, d, f, q, r, n, s
- ZN · Zinc ion · metal · 6 copies · chains O, c, s, d
- CYN · Cyanide ion · ion · 36 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, P, Q, R, S, T, U, V, W, X, Y, Z, a, e, f, g, h, i, j, k, l, m, n, o, p
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 | 897 | 0.85 | 0.86 | 65 | HEM, CYN |
| 2 | 865 | 0.85 | 0.86 | 64 | HEM, CYN |
| 3 | 847 | 0.85 | 0.87 | 61 | HEM, CYN |
| 4 | 889 | 0.85 | 0.86 | 63 | HEM, CYN |
| 5 | 884 | 0.85 | 0.86 | 64 | HEM, CYN |
Interfaces
119 interfaces between chains.
- b–c · 1482 Ų buried · 10 hydrogen bonds · protein-protein
- q–r · 1463 Ų buried · 9 hydrogen bonds · protein-protein
- M–N · 1457 Ų buried · 9 hydrogen bonds · protein-protein
- c–d · 1394 Ų buried · 16 hydrogen bonds · protein-protein
- N–O · 1375 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 96 disulfide, 3 glycan, 2 cofactor, 1 isopeptide (disulfide, N-glycosylation, heme attachment, isopeptide).
Compared structures
- 4U8U · The Crystallographic structure of the giant hemoglobin from Glossoscolex paulistus at 3.2… · the same entry in another collection · chain U against U, 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
- Elsewhere: RCSB PDB 4U8U · PDBe 4U8U
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