Research workbench

Co bound as bridging ligand at the active site of vanadium nitrogenase vfe protein

Analyse Co bound as bridging ligand at the active site of vanadium nitrogenase vfe… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7ADR
Type: protein
Length: 2,101 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nitrogenase vanadium-iron protein alpha chain; Nitrogenase vanadium-iron protein beta…
EC: 1.18.6.1
UniProt: P16855, P16856, P16857
Ligands: D6N, HCA, BCT, CLF, MG, CMO
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 5 distinct chains · 52% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Nitrogenase vanadium-iron protein alpha chain (EC 1.18.6.1)	protein	473	48% helix, 15% strand	P16855
B	Nitrogenase vanadium-iron protein beta chain (EC 1.18.6.1)	protein	465	49% helix, 14% strand	P16856
C	Nitrogenase vanadium-iron protein delta chain (EC 1.18.6.1)	protein	113	73% helix, 0% strand	P16857
E	Nitrogenase vanadium-iron protein beta chain (EC 1.18.6.1)	protein	466	49% helix, 14% strand	P16856
F	Nitrogenase vanadium-iron protein delta chain (EC 1.18.6.1)	protein	111	71% helix, 0% strand	P16857

Ligands and binding sites

D6N · FeV · ligand · 2 copies · chains A, D
HCA · 3-hydroxy-3-carboxy-adipic acid · ligand · 2 copies · chains A, B, D, E
BCT · Bicarbonate ion · ligand · 2 copies · chains A, D
CLF · FE(8)-S(7) cluster · ligand · 2 copies · chains A, B, D, E
MG · Magnesium ion · metal · 4 copies · chains A, B, E, D, C, F
CMO · Carbon monoxide · ion · 2 copies · chains A, D
EDO · 1,2-ethanediol · additive · 9 copies · chains B, A, C, E, D, F
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains A, B, D, E

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	384	0.86	0.95	51	D6N, HCA, BCT, CMO
2	371	0.86	0.94	48	D6N, HCA, BCT, CMO
3	1166	0.84	0.85	89	empty
4	65	0.75	0.99	25	CLF
5	73	0.74	0.98	19	empty

Interfaces

7 interfaces between chains.

A–B · 3353 Å² buried · 52 hydrogen bonds · protein-protein
D–E · 3345 Å² buried · 50 hydrogen bonds · protein-protein
B–E · 2352 Å² buried · 40 hydrogen bonds · protein-protein
A–C · 1753 Å² buried · 32 hydrogen bonds · protein-protein
B–D · 1741 Å² buried · 29 hydrogen bonds · protein-protein

Compared structures

7ADR · CO bound as bridging ligand at the active site of vanadium nitrogenase VFe protein · the same entry in another collection · chain F against F, TM-score 1.00
P16856 · AlphaFold monomer V2.0 prediction for nitrogenase vanadium-iron protein beta chain… · a predicted model of the same protein · chain E against A, TM-score 0.99
P16855 · AlphaFold monomer V2.0 prediction for nitrogenase vanadium-iron protein alpha chain… · a predicted model of the same protein · chain A against A, TM-score 0.99
P16857 · AlphaFold monomer V2.0 prediction for nitrogenase vanadium-iron protein delta chain… · a predicted model of the same protein · chain C against A, TM-score 0.98

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 P16855
Every structure of UniProt P16856
Every structure of UniProt P16857
Elsewhere: RCSB PDB 7ADR · PDBe 7ADR · UniProt P16855 · UniProt P16856 · UniProt P16857

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