MolNFT v1 · #32237 · protein

Q69E-FESOD

2BKB · Superoxide dismutase [fe]: “Q69E-FESOD”. X-ray diffraction, 1 ligand (FE2), 6 pockets (best druggability 0.59). MolNFT v1 #32237 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2BKB
Type: protein
Length: 768 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Superoxide dismutase [fe]
EC: 1.15.1.1
UniProt: P0AGD3
Ligands: FE2
Pockets: 6 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 52% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Superoxide dismutase [fe] (EC 1.15.1.1)	protein	192	52% helix, 12% strand	P0AGD3

Ligands and binding sites

FE2 · Fe (II) ion · metal · 4 copies · chains A, B, C, D

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

Pockets

6 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	205	0.59	0.81	23	empty
2	188	0.59	0.81	24	empty
3	222	0.58	0.80	20	empty
4	214	0.57	0.79	21	empty
5	182	0.45	0.74	24	empty

Interfaces

4 interfaces between chains.

C–D · 980 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 979 Å² buried · 16 hydrogen bonds · protein-protein
B–D · 173 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 167 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

2BKB · q69e-FeSOD · the same entry in another collection · chain A against A, TM-score 1.00
P0AGD3 · AlphaFold monomer V2.0 prediction for superoxide dismutase [fe] (P0AGD3) · 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 P0AGD3
Elsewhere: RCSB PDB 2BKB · PDBe 2BKB · UniProt P0AGD3

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