Research workbench

Human zeta-2 beta-2-S hemoglobin

Analyse Human zeta-2 beta-2-S hemoglobin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3W4U
Type: protein
Length: 855 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemoglobin subunit zeta; Hemoglobin subunit beta
UniProt: P02008, P68871
Ligands: HEM, CMO
Pockets: 15 · best druggability 0.86

Structure

x-ray diffraction · 3 distinct chains · 78% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Hemoglobin subunit zeta	protein	141	76% helix, 0% strand	P02008
B, D, F	Hemoglobin subunit beta	protein	145	79% helix, 0% strand	P68871
E	Hemoglobin subunit zeta	protein	138	78% helix, 0% strand	P02008

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 6 copies · chains A, B, C, D, E, F
CMO · Carbon monoxide · ion · 6 copies · chains A, B, C, D, E, F

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

Pockets

15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1090	0.86	0.87	123	empty
2	230	0.74	0.88	28	HEM, CMO
3	237	0.73	0.87	28	HEM, CMO
4	225	0.72	0.87	28	HEM, CMO
5	202	0.71	0.87	25	HEM, CMO

Interfaces

11 interfaces between chains.

E–F · 882 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 872 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 869 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 581 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 548 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

3W4U · Human zeta-2 beta-2-s hemoglobin · the same entry in another collection · chain F against F, TM-score 1.00
P02008 · AlphaFold monomer V2.0 prediction for hemoglobin subunit zeta (P02008) · a predicted model of the same protein · chain E against A, TM-score 0.98

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 P02008
Every structure of UniProt P68871
Elsewhere: RCSB PDB 3W4U · PDBe 3W4U · UniProt P02008 · UniProt P68871

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