MolNFT v1 · #115891 · protein

Nitrogenase molybdenum-iron protein beta-K400E mutant

5CX1 · Nitrogenase molybdenum-iron protein alpha chain: “Nitrogenase molybdenum-iron protein beta-K400E mutant”. X-ray diffraction, 4 ligands (HCA, ICS, CLF), 20 pockets (best druggability 0.88). MolNFT v1 #115891 on GenesisL1: 3D…

PDB: 5CX1
Type: protein
Length: 7,992 residues
Chains: 16
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
Ligands: HCA, ICS, CLF, CA
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 2 distinct chains · 50% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G, I, K, M, O	Nitrogenase molybdenum-iron protein alpha chain (EC 1.18.6.1)	protein	477	47% helix, 14% strand	P07328
B, D, F, H, J, L, N, P	Nitrogenase molybdenum-iron protein beta chain (EC 1.18.6.1)	protein	522	52% helix, 10% strand	P07329

Ligands and binding sites

HCA · 3-hydroxy-3-carboxy-adipic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H, I, J, K, M, N, O, P
ICS · iron-sulfur-molybdenum cluster with interstitial carbon · ligand · 8 copies · chains A, C, E, G, I, K, M, O
CLF · FE(8)-S(7) cluster · ligand · 8 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
CA · Calcium ion · metal · 8 copies · chains B, C, D, A, F, G, H, E, J, K, L, I, N, O, P, M

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	549	0.88	0.94	76	HCA, ICS
2	549	0.88	0.94	77	HCA, ICS
3	550	0.88	0.94	77	HCA, ICS
4	547	0.88	0.94	78	HCA, ICS
5	549	0.88	0.94	77	HCA, ICS

Interfaces

32 interfaces between chains.

E–F · 4739 Å² buried · 57 hydrogen bonds · protein-protein
M–N · 4732 Å² buried · 58 hydrogen bonds · protein-protein
I–J · 4730 Å² buried · 59 hydrogen bonds · protein-protein
K–L · 4725 Å² buried · 59 hydrogen bonds · protein-protein
C–D · 4720 Å² buried · 57 hydrogen bonds · protein-protein

Compared structures

5CX1 · Nitrogenase molybdenum-iron protein beta-K400E mutant · the same entry in another collection · chain P against P, 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 P07328
Every structure of UniProt P07329
Elsewhere: RCSB PDB 5CX1 · PDBe 5CX1 · UniProt P07328 · UniProt P07329

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