MolNFT v1 · #109324 · protein

Crystal structure of mgamppcp-bound AV2-AV1 complex

4WZB · Nitrogenase molybdenum-iron protein alpha chain: “Crystal structure of mgamppcp-bound AV2-AV1 complex”. X-ray diffraction, 7 ligands (ACP, HCA, ICS), 20 pockets (best druggability 0.88). MolNFT v1 #109324 on GenesisL1: 3D structure…

PDB: 4WZB
Type: protein
Length: 3,064 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nitrogenase molybdenum-iron protein alpha chain; Nitrogenase molybdenum-iron protein beta…
EC: 1.18.6.1
UniProt: P07328, P07329, P00459
Ligands: ACP, HCA, ICS, CLF, SF4, MG, FE2
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 7 distinct chains · 47% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nitrogenase molybdenum-iron protein alpha chain (EC 1.18.6.1)	protein	477	48% helix, 14% strand	P07328
B, D	Nitrogenase molybdenum-iron protein beta chain (EC 1.18.6.1)	protein	522	51% helix, 11% strand	P07329
C	Nitrogenase molybdenum-iron protein alpha chain (EC 1.18.6.1)	protein	476	49% helix, 14% strand	P07328
E	Nitrogenase iron protein 1 (EC 1.18.6.1)	protein	270	43% helix, 17% strand	P00459
F	Nitrogenase iron protein 1 (EC 1.18.6.1)	protein	263	43% helix, 18% strand	P00459
G	Nitrogenase iron protein 1 (EC 1.18.6.1)	protein	272	45% helix, 17% strand	P00459
H	Nitrogenase iron protein 1 (EC 1.18.6.1)	protein	262	42% helix, 18% strand	P00459

Ligands and binding sites

ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 4 copies · chains E, F, G, H
HCA · 3-hydroxy-3-carboxy-adipic acid · ligand · 2 copies · chains A, B, C, D
ICS · iron-sulfur-molybdenum cluster with interstitial carbon · ligand · 2 copies · chains A, C
CLF · FE(8)-S(7) cluster · ligand · 2 copies · chains A, B, C, D
SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B, E, F, C, D, G, H
MG · Magnesium ion · metal · 4 copies · chains E, F, G, H
FE2 · Fe (II) ion · metal · 2 copies · chains B, C, D, A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	557	0.88	0.94	74	HCA, ICS
2	541	0.88	0.94	74	HCA, ICS
3	1176	0.85	0.86	77	empty
4	862	0.83	0.85	93	MG, ACP
5	1103	0.81	0.82	82	empty

Interfaces

15 interfaces between chains.

A–B · 4765 Å² buried · 55 hydrogen bonds · protein-protein
C–D · 4764 Å² buried · 54 hydrogen bonds · protein-protein
B–D · 3182 Å² buried · 62 hydrogen bonds · protein-protein
G–H · 1648 Å² buried · 16 hydrogen bonds · protein-protein
E–F · 1634 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

4WZB · Crystal Structure of MgAMPPCP-bound Av2-Av1 complex · the same entry in another collection · chain H against H, TM-score 1.00
P07328 · AlphaFold monomer V2.0 prediction for nitrogenase molybdenum-iron protein alpha chain… · a predicted model of the same protein · chain C against A, TM-score 1.00
P07329 · AlphaFold monomer V2.0 prediction for nitrogenase molybdenum-iron protein beta chain… · a predicted model of the same protein · chain B against A, TM-score 1.00
P00459 · AlphaFold monomer V2.0 prediction for nitrogenase iron protein 1 (P00459) · a predicted model of the same protein · chain G 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 P07328
Every structure of UniProt P07329
Every structure of UniProt P00459
Elsewhere: RCSB PDB 4WZB · PDBe 4WZB · UniProt P07328 · UniProt P07329 · UniProt P00459

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