MolNFT v1 · #108640 · protein

Crystal structure of human HO1 H25R

4WD4 · Heme oxygenase 1: “Crystal structure of human HO1 H25R”. X-ray diffraction, 1 ligand (HEM), 11 pockets (best druggability 0.74). MolNFT v1 #108640 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4WD4
Type: protein
Length: 856 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heme oxygenase 1
EC: 1.14.99.3
UniProt: P09601
Ligands: HEM
Pockets: 11 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 74% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Heme oxygenase 1 (EC 1.14.99.3)	protein	214	74% helix, 0% strand	P09601

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains B, D

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

Pockets

11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	324	0.74	0.85	37	HEM
2	347	0.73	0.84	36	HEM
3	320	0.72	0.85	36	HEM
4	341	0.72	0.84	35	HEM
5	654	0.72	0.79	51	empty

Interfaces

4 interfaces between chains.

C–D · 1140 Å² buried · 29 hydrogen bonds · protein-protein
A–B · 1137 Å² buried · 28 hydrogen bonds · protein-protein
B–D · 353 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 34 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4WD4 · Crystal structure of human HO1 H25R · the same entry in another collection · chain A against A, TM-score 1.00
P09601 · AlphaFold monomer V2.0 prediction for heme oxygenase 1 (P09601) · a predicted model of the same protein · chain A 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 P09601
Elsewhere: RCSB PDB 4WD4 · PDBe 4WD4 · UniProt P09601

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