MolNFT v1 · #10492 · protein

Hagfish co ligand hemoglobin

1IT3: “Hagfish co ligand hemoglobin”. X-ray diffraction, 2 ligands (HEM, CMO), 9 pockets (best druggability 0.74). MolNFT v1 #10492 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1IT3
Type: protein
Length: 584 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemoglobin
UniProt: Q7SID0
Ligands: HEM, CMO
Pockets: 9 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 70% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Hemoglobin	protein	146	70% helix, 0% strand	Q7SID0

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
CMO · Carbon monoxide · ion · 4 copies · chains A, B, C, D

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	262	0.74	0.87	29	HEM, CMO
2	251	0.74	0.87	30	HEM, CMO
3	277	0.73	0.86	31	HEM, CMO
4	641	0.72	0.79	56	empty
5	241	0.72	0.86	27	HEM, CMO

Interfaces

5 interfaces between chains.

A–D · 415 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 395 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 384 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 319 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 162 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

1IT3 · Hagfish CO ligand hemoglobin · the same entry in another collection · chain D against D, TM-score 1.00
Q7SID0 · AlphaFold monomer V2.0 prediction for globin-F1 (Q7SID0) · a predicted model of the same protein · chain D 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 Q7SID0
Elsewhere: RCSB PDB 1IT3 · PDBe 1IT3 · UniProt Q7SID0

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