MolNFT v1 · #94270 · protein

Scapharca tetrameric hemoglobin, co-state

4HRR · Globin-2 a chain: “Scapharca tetrameric hemoglobin, co-state”. X-ray diffraction, 3 ligands (HEM, ACE, CMO), 9 pockets (best druggability 0.87). MolNFT v1 #94270 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4HRR
Type: protein
Length: 1,199 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, CMO
Pockets: 9 · best druggability 0.87

Structure

x-ray diffraction · 3 distinct chains · 83% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	Globin-2 a chain	protein	149	85% helix, 0% strand	P14821
B, D, F	Hemoglobin B chain	protein	151	81% helix, 0% strand	O02480
H	Hemoglobin B chain	protein	150	85% 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 · 4 copies · chains A, C, E, G
CMO · Carbon monoxide · ion · 8 copies · chains A, B, C, D, E, F, G, H

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	765	0.87	0.90	69	HEM, CMO
2	878	0.87	0.88	69	HEM, CMO
3	906	0.87	0.88	71	HEM, CMO
4	875	0.86	0.87	71	HEM, CMO
5	1128	0.74	0.78	87	empty

Interfaces

11 interfaces between chains.

C–D · 1004 Å² buried · 7 hydrogen bonds · protein-protein
E–F · 1003 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 1001 Å² buried · 8 hydrogen bonds · protein-protein
G–H · 999 Å² buried · 7 hydrogen bonds · protein-protein
E–H · 617 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

4HRR · Scapharca tetrameric hemoglobin, CO-state · 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 G against A, TM-score 0.99

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 4HRR · PDBe 4HRR · UniProt P14821 · UniProt O02480

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