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Bacterial dimeric hemoglobin from vitreoscilla stercoraria

Analyse Bacterial dimeric hemoglobin from vitreoscilla stercoraria in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1VHB
Type: protein
Length: 270 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemoglobin
UniProt: P04252
Ligands: HEM
Pockets: 4 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 87% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Hemoglobin	protein	135	87% helix, 0% strand	P04252

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	417	0.73	0.83	34	empty
2	223	0.69	0.85	29	HEM
3	225	0.69	0.85	28	HEM
4	180	0.56	0.80	20	empty

Interfaces

1 interface between chains.

A–B · 459 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

1VHB · Bacterial dimeric hemoglobin from vitreoscilla stercoraria · the same entry in another collection · chain A against A, TM-score 1.00
P04252 · AlphaFold monomer V2.0 prediction for bacterial hemoglobin (P04252) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 P04252
Elsewhere: RCSB PDB 1VHB · PDBe 1VHB · UniProt P04252

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