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A zn-mediated tetrahedral protein lattice cage

Analyse A zn-mediated tetrahedral protein lattice cage in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3M4B
Type: protein
Length: 424 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Soluble cytochrome B562
UniProt: P0ABE7
Ligands: HEM, ZN
Pockets: 8 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 81% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Soluble cytochrome B562	protein	106	81% helix, 0% strand	P0ABE7

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
ZN · Zinc ion · metal · 12 copies · chains A, B, D, C
ACT · Acetate ion · additive · 4 copies · chains A, B, C, D

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

Pockets

8 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	358	0.63	0.79	48	empty
2	158	0.61	0.83	23	HEM
3	135	0.60	0.84	21	HEM
4	269	0.56	0.77	36	empty
5	167	0.56	0.80	24	HEM

Interfaces

5 interfaces between chains.

C–D · 425 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 333 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 135 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 130 Å² buried · 1 hydrogen bond · protein-protein
A–B · 128 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 cofactor, 4 covalent (heme attachment, additive adduct).

Compared structures

3M4B · A Zn-mediated tetrahedral protein lattice cage · the same entry in another collection · chain D against D, TM-score 1.00
P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain D 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 P0ABE7
Elsewhere: RCSB PDB 3M4B · PDBe 3M4B · UniProt P0ABE7

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