MolNFT v1 · #69819 · protein

E. COLI nrfa sulfite ocmplex

3L1T · Cytochrome C-552: “E. COLI nrfa sulfite ocmplex”. X-ray diffraction, 3 ligands (HEC, CA, SO3), 20 pockets (best druggability 0.89). MolNFT v1 #69819 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3L1T
Type: protein
Length: 1,764 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome C-552
EC: 1.7.2.2
UniProt: P0ABK9
Ligands: HEC, CA, SO3
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 1 distinct chain · 56% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Cytochrome C-552 (EC 1.7.2.2)	protein	441	56% helix, 5% strand	P0ABK9

Ligands and binding sites

HEC · Heme C · ligand · 20 copies · chains A, B, C, D
CA · Calcium ion · metal · 8 copies · chains A, B, C, D
SO3 · Sulfite ion · ion · 5 copies · chains A, B, C, D
EDO · 1,2-ethanediol · additive · 12 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	945	0.89	0.91	128	HEC, SO3, EDO
2	839	0.88	0.91	107	HEC, SO3
3	615	0.88	0.93	93	HEC, SO3
4	310	0.82	0.93	45	HEC, SO3
5	174	0.78	0.93	38	HEC

Interfaces

4 interfaces between chains.

A–B · 1567 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 1544 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 415 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 40 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 32 cofactor (heme c attachment).

Compared structures

3L1T · E. coli NrfA sulfite ocmplex · the same entry in another collection · chain A against A, TM-score 1.00
P0ABK9 · AlphaFold monomer V2.0 prediction for cytochrome C-552 (P0ABK9) · a predicted model of the same protein · 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 P0ABK9
Elsewhere: RCSB PDB 3L1T · PDBe 3L1T · UniProt P0ABK9

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.