MolNFT v1 · #150641 · protein

Ferric dtpa from streptomyces lividans

6GZW · Dye type peroxidase a: “Ferric dtpa from streptomyces lividans”. X-ray diffraction, 1 ligand (HEM), 11 pockets (best druggability 0.82). MolNFT v1 #150641 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6GZW
Type: protein
Length: 740 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dye type peroxidase a
UniProt: A0A076MAJ9
Ligands: HEM
Pockets: 11 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 28% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dye type peroxidase a	protein	370	29% helix, 23% strand	A0A076MAJ9
B	Dye type peroxidase a	protein	370	27% helix, 23% strand	A0A076MAJ9

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

11 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	340	0.82	0.92	45	HEM
2	344	0.81	0.91	47	HEM
3	376	0.61	0.77	47	empty
4	363	0.61	0.77	48	empty
5	141	0.52	0.80	23	empty

Interfaces

1 interface between chains.

A–B · 2748 Å² buried · 44 hydrogen bonds · protein-protein

Compared structures

6GZW · Ferric DtpA from Streptomyces lividans · the same entry in another collection · 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 A0A076MAJ9
Elsewhere: RCSB PDB 6GZW · PDBe 6GZW · UniProt A0A076MAJ9

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