MolNFT v1 · #9137 · protein

The structure of deoxy and oxy hemerythrin at 2.0 ångströms resolution

1HMD: “The structure of deoxy and oxy hemerythrin at 2.0 ångströms resolution”. X-ray diffraction, 2 ligands (ACE, FEO), 5 pockets (best druggability 0.53). MolNFT v1 #9137 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1HMD
Type: protein
Length: 452 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemerythrin
UniProt: P02246
Ligands: ACE, FEO
Pockets: 5 · best druggability 0.53

Structure

x-ray diffraction · 1 distinct chain · 72% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Hemerythrin	protein	113	72% helix, 0% strand	P02246

Ligands and binding sites

ACE · Acetyl group · ligand · 4 copies · chains A, B, C, D
FEO · Mu-oxo-diiron · ligand · 4 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	288	0.53	0.75	29	empty
2	68	0.36	0.78	12	empty
3	54	0.32	0.77	14	empty
4	52	0.29	0.75	15	empty
5	58	0.28	0.73	12	empty

Interfaces

3 interfaces between chains.

C–D · 947 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 213 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 167 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

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

Compared structures

1HMD · The structure of deoxy and oxy hemerythrin at 2.0 ångströms resolution · the same entry in another collection · chain B against B, TM-score 1.00
P02246 · AlphaFold monomer V2.0 prediction for hemerythrin (P02246) · 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 P02246
Elsewhere: RCSB PDB 1HMD · PDBe 1HMD · UniProt P02246

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