Research workbench

DYP2 from amycolatopsis sp. atcc 39116

Analyse DYP2 from amycolatopsis sp. atcc 39116 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4G2C
Type: protein
Length: 925 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DYP2
EC: 1.-.-.-
Ligands: HEM, MN
Pockets: 10 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DYP2 (EC 1.-.-.-)	protein	462	31% helix, 19% strand	—
B	DYP2 (EC 1.-.-.-)	protein	463	31% helix, 19% strand	—

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
MN · Manganese (II) ion · metal · 2 copies · chains A, B
ACT · Acetate ion · additive · 38 copies · chains A, B

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

Pockets

10 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	200	0.83	0.97	37	ACT
2	1026	0.82	0.83	93	HEM, ACT
3	1046	0.80	0.82	93	HEM, ACT
4	215	0.53	0.77	29	MN
5	225	0.53	0.77	31	MN, ACT

Interfaces

1 interface between chains.

A–B · 1011 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

4G2C · DyP2 from Amycolatopsis sp. ATCC 39116 · 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
Elsewhere: RCSB PDB 4G2C · PDBe 4G2C

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