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Scapharca tetrameric hemoglobin, unliganded

Analyse Scapharca tetrameric hemoglobin, unliganded in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4HRT
Type: protein
Length: 1,193 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Globin-2 a chain; Hemoglobin B chain
UniProt: P14821, O02480
Ligands: HEM, ACE, PO4
Pockets: 9 · best druggability 0.87

Structure

x-ray diffraction · 4 distinct chains · 84% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	Globin-2 a chain	protein	149	86% helix, 0% strand	P14821
B	Hemoglobin B chain	protein	147	82% helix, 0% strand	O02480
D, F	Hemoglobin B chain	protein	151	84% helix, 0% strand	O02480
H	Hemoglobin B chain	protein	148	82% helix, 0% strand	O02480

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains A, B, C, D, E, F, G, H
ACE · Acetyl group · ligand · 6 copies · chains A, C, D, E, G, H
PO4 · Phosphate ion · ion · chains E

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1140	0.87	0.88	85	HEM
2	867	0.87	0.88	69	HEM
3	887	0.87	0.88	70	HEM
4	917	0.86	0.88	68	HEM
5	816	0.72	0.78	65	empty

Interfaces

11 interfaces between chains.

G–H · 1050 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 1050 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 1049 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 1044 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 598 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 covalent (covalent ligand).

Compared structures

4HRT · Scapharca tetrameric hemoglobin, unliganded · the same entry in another collection · chain H against H, TM-score 1.00
P14821 · AlphaFold monomer V2.0 prediction for globin-2 a chain (P14821) · a predicted model of the same protein · chain A against A, 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 P14821
Every structure of UniProt O02480
Elsewhere: RCSB PDB 4HRT · PDBe 4HRT · UniProt P14821 · UniProt O02480

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