MolNFT v1 · #27220 · protein

Crystal structure of the nitrogenase fe protein ASP39ASN

1XD8 · Nitrogenase iron protein 1: “Crystal structure of the nitrogenase fe protein ASP39ASN”. X-ray diffraction, 1 ligand (SF4), 2 pockets (best druggability 0.81). MolNFT v1 #27220 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 1XD8
Type: protein
Length: 578 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nitrogenase iron protein 1
EC: 1.18.6.1
UniProt: P00459
Ligands: SF4
Pockets: 2 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Nitrogenase iron protein 1 (EC 1.18.6.1)	protein	289	39% helix, 16% strand	P00459

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1120	0.81	0.83	122	empty
2	81	0.49	0.83	18	empty

Interfaces

1 interface between chains.

A–B · 1899 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

1XD8 · Crystal Structure of the Nitrogenase Fe protein Asp39Asn · the same entry in another collection · chain A 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 A against A, TM-score 0.95

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 P00459
Elsewhere: RCSB PDB 1XD8 · PDBe 1XD8 · UniProt P00459

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