MolNFT v1 · #25777 · protein

Photosystem II from thermosynechococcus elongatus

1W5C · Photosystem Q(B) protein 1: “Photosystem II from thermosynechococcus elongatus”. X-ray diffraction, 8 ligands (CLA, PHO, PL9), 20 pockets (best druggability 0.86). MolNFT v1 #25777 on GenesisL1: 3D structure, binding sites and…

PDB: 1W5C
Type: protein
Length: 4,972 residues
Chains: 20
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Photosystem Q(B) protein 1; Photosystem II core light harvesting protein; Photosystem II…
UniProt: P0A444, Q8DIQ1, Q8DIF8, Q8CM25, P12238, P12239, P56150
Ligands: CLA, PHO, PL9, HEM, BCR, HEC, MN, FE2
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 11 distinct chains · 48% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G	Photosystem Q(B) protein 1	protein	332	53% helix, 2% strand	P0A444
B	Photosystem II core light harvesting protein	protein	479	41% helix, 4% strand	Q8DIQ1
C, I	Photosystem II CP43 protein	protein	438	47% helix, 0% strand	Q8DIF8
D, J	Photosystem II reaction center D2 protein	protein	350	55% helix, 1% strand	Q8CM25
E, K	Cytochrome B559 alpha subunit	protein	76	62% helix, 0% strand	P12238
F, L	Cytochrome B559 beta subunit	protein	37	62% helix, 0% strand	P12239
H	Photosystem II core light harvesting protein	protein	479	42% helix, 4% strand	Q8DIQ1
O, P	Photosystem II manganese-stabilizing polypeptide	protein	179	2% helix, 32% strand	—
S, U	Photosystem II 12 kda extrinsic protein	protein	100	42% helix, 4% strand	—
T, V	Cytochrome C-550	protein	136	47% helix, 6% strand	P56150
X, Y	Unassigned subunits	protein	359	76% helix, 0% strand	—

Ligands and binding sites

CLA · Chlorophyll A · ligand · 70 copies · chains A, D, X, B, C, G, J, Y, H, I
PHO · Pheophytin A · ligand · 4 copies · chains A, D, G, J
PL9 · 2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2, 6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone · ligand · 2 copies · chains D, J
HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains E, F, X, K, L, Y
BCR · Beta-carotene · ligand · 2 copies · chains D, F, J, L
HEC · Heme C · ligand · 2 copies · chains T, V
MN · Manganese (II) ion · metal · 8 copies · chains A, G
FE2 · Fe (II) ion · metal · 2 copies · chains A, D, G, J

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	613	0.86	0.91	94	empty
2	923	0.86	0.88	102	HEC
3	667	0.86	0.90	134	MN
4	541	0.85	0.90	75	HEC
5	522	0.83	0.89	102	MN

Interfaces

67 interfaces between chains.

G–J · 4639 Å² buried · 36 hydrogen bonds · protein-protein
A–D · 4623 Å² buried · 37 hydrogen bonds · protein-protein
H–J · 2381 Å² buried · 18 hydrogen bonds · protein-protein
B–D · 2371 Å² buried · 18 hydrogen bonds · protein-protein
G–I · 1980 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 cofactor (heme c attachment).

Compared structures

1W5C · Photosystem II from Thermosynechococcus elongatus · the same entry in another collection · chain J against J, 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 P0A444
Every structure of UniProt Q8DIQ1
Every structure of UniProt Q8DIF8
Every structure of UniProt Q8CM25
Every structure of UniProt P12238
Every structure of UniProt P12239
Every structure of UniProt P56150
Elsewhere: RCSB PDB 1W5C · PDBe 1W5C · UniProt P0A444 · UniProt Q8DIQ1 · UniProt Q8DIF8 · UniProt Q8CM25 · UniProt P12238 · UniProt P12239 · UniProt P56150

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