MolNFT v1 · #55543 · protein

Structure of the ADPXALF3-stabilized transition state of the nitrogenase-like dark-operative protochlorophyllide oxidoreductase complex from prochlorococcus marinus with its substrate protochlorophyllide a

2YNM · Light-independent protochlorophyllide reductase iron-sulfur…: “Structure of the ADPXALF3-stabilized transition state of the nitrogenase-like dark-operative…”. X-ray diffraction, 6 ligands (AF3, ADP, SF4), 13 pockets (best…

PDB: 2YNM
Type: protein
Length: 1,440 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein…
EC: 1.3.7.7, 1.18.-.-
UniProt: Q7VD39, Q7VD37, Q7VD38
Ligands: AF3, ADP, SF4, PMR, MG, K
Pockets: 13 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 48% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein (EC 1.3.7.7, 1.18.-.-)	protein	267	44% helix, 18% strand	Q7VD39
B	Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein (EC 1.3.7.7, 1.18.-.-)	protein	268	44% helix, 17% strand	Q7VD39
C	Light-independent protochlorophyllide reductase subunit N (EC 1.3.7.7, 1.18.-.-)	protein	417	47% helix, 19% strand	Q7VD37
D	Light-independent protochlorophyllide reductase subunit B (EC 1.3.7.7, 1.18.-.-)	protein	488	52% helix, 12% strand	Q7VD38

Ligands and binding sites

AF3 · Aluminum fluoride · ligand · 2 copies · chains A, B
ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B, C, D
PMR · Protochlorophyllide · ligand · chains C, D
MG · Magnesium ion · metal · 2 copies · chains A, B
K · Potassium ion · metal · chains C, D
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 4 copies · chains A, B, C, D
1PE · Pentaethylene glycol · additive · chains A, D

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

Pockets

13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1098	0.83	0.84	100	empty
2	478	0.82	0.89	70	AF3, ADP, MG, GOL, EPE
3	76	0.74	0.97	24	GOL
4	690	0.73	0.79	68	K, GOL
5	338	0.69	0.82	55	EPE

Interfaces

6 interfaces between chains.

C–D · 2743 Å² buried · 45 hydrogen bonds · protein-protein
A–B · 2272 Å² buried · 28 hydrogen bonds · protein-protein
B–C · 755 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 662 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 471 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

2YNM · Structure of the ADPxAlF3-Stabilized Transition State of the Nitrogenase-like… · the same entry in another collection · chain D against D, TM-score 1.00
Q7VD39 · AlphaFold monomer V2.0 prediction for light-independent protochlorophyllide reductase… · a predicted model of the same protein · chain A against A, TM-score 0.98
Q7VD37 · AlphaFold monomer V2.0 prediction for light-independent protochlorophyllide reductase… · a predicted model of the same protein · chain C against A, TM-score 0.97
Q7VD38 · AlphaFold monomer V2.0 prediction for light-independent protochlorophyllide reductase… · a predicted model of the same protein · chain D against A, TM-score 0.93

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 Q7VD39
Every structure of UniProt Q7VD37
Every structure of UniProt Q7VD38
Elsewhere: RCSB PDB 2YNM · PDBe 2YNM · UniProt Q7VD39 · UniProt Q7VD37 · UniProt Q7VD38

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