Research workbench

Crystal structure of the psbm-deletion mutant of photosystem II

Analyse Crystal structure of the psbm-deletion mutant of photosystem II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5H2F
Type: protein
Length: 5,151 residues
Chains: 36
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Photosystem II protein D1 1; Photosystem II CP47 reaction center protein; Photosystem II…
EC: 1.10.3.9
UniProt: P0A444, Q8DIQ1, Q8DIF8, Q8CM25, Q8DIP0, Q8DIN9, Q8DJ43, Q8DJZ6, P59087, Q9F1K9, Q8DIN8, P0A431, Q8DIQ0, Q9F1L5, P0A386, Q8DJI1, Q9F1R6, Q8DHJ2
Ligands: CLA, UNL, BCR, LMG, LHG, DGD, SQD, PHO, PL9, OEX, BCT, HEM, RRX, HEC, CA, MG…
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 28 distinct chains · 55% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, a	Photosystem II protein D1 1 (EC 1.10.3.9)	protein	334	59% helix, 4% strand	P0A444
B	Photosystem II CP47 reaction center protein	protein	505	50% helix, 12% strand	Q8DIQ1
C	Photosystem II CP43 reaction center protein	protein	451	57% helix, 6% strand	Q8DIF8
D	Photosystem II D2 protein (EC 1.10.3.9)	protein	342	64% helix, 4% strand	Q8CM25
E	Cytochrome B559 subunit alpha	protein	79	57% helix, 0% strand	Q8DIP0
F	Cytochrome B559 subunit beta	protein	33	70% helix, 0% strand	Q8DIN9
H	Photosystem II reaction center protein H	protein	63	51% helix, 3% strand	Q8DJ43
I	Photosystem II reaction center protein I	protein	35	74% helix, 0% strand	Q8DJZ6
J	Photosystem II reaction center protein J	protein	36	64% helix, 0% strand	P59087
K, k	Photosystem II reaction center protein K	protein	37	81% helix, 0% strand	Q9F1K9
L, l	Photosystem II reaction center protein L	protein	35	66% helix, 6% strand	Q8DIN8
O, o	Photosystem II manganese-stabilizing polypeptide	protein	243	7% helix, 46% strand	P0A431
T, t	Photosystem II reaction center protein T	protein	30	70% helix, 0% strand	Q8DIQ0
U, u	Photosystem II 12 kda extrinsic protein	protein	97	49% helix, 4% strand	Q9F1L5
V, v	Cytochrome C-550	protein	137	48% helix, 6% strand	P0A386
Y, y	Photosystem II reaction center protein YCF12	protein	29	79% helix, 0% strand	Q8DJI1
X	Photosystem II reaction center X protein	protein	37	81% helix, 0% strand	Q9F1R6
Z	Photosystem II reaction center protein Z	protein	62	87% helix, 0% strand	Q8DHJ2
b	Photosystem II CP47 reaction center protein	protein	483	50% helix, 11% strand	Q8DIQ1
c	Photosystem II CP43 reaction center protein	protein	455	57% helix, 6% strand	Q8DIF8
d	Photosystem II D2 protein (EC 1.10.3.9)	protein	341	65% helix, 3% strand	Q8CM25
e	Cytochrome B559 subunit alpha	protein	79	54% helix, 0% strand	Q8DIP0
f	Cytochrome B559 subunit beta	protein	31	74% helix, 0% strand	Q8DIN9
h	Photosystem II reaction center protein H	protein	62	53% helix, 3% strand	Q8DJ43
i	Photosystem II reaction center protein I	protein	36	72% helix, 0% strand	Q8DJZ6
j	Photosystem II reaction center protein J	protein	40	58% helix, 0% strand	P59087
x	Photosystem II reaction center X protein	protein	36	83% helix, 0% strand	Q9F1R6
z	Photosystem II reaction center protein Z	protein	61	85% helix, 0% strand	Q8DHJ2

Ligands and binding sites

CLA · Chlorophyll A · ligand · 70 copies · chains A, D, T, I, B, H, L, C, K, Y, Z, X, a, d, t, l, i, b, h, c, k, y, z, x
UNL · Unknown ligand · ligand · 27 copies · chains A, b, B, O, D, H, X, I, J, T, U, Z, a, i, c, d, x, j, t, u
BCR · Beta-carotene · ligand · 18 copies · chains A, I, B, t, C, K, Z, D, F, J, Y, a, i, T, b, c, k, z, d, f, j, y
LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 12 copies · chains A, C, I, B, D, L, J, K, Y, Z, H, X, F, b, d, l, c, j, k, y, z, h, x, a, i, f
LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 12 copies · chains A, C, D, K, B, L, T, a, i, b, d, l, c, k, t
DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · 10 copies · chains A, C, J, D, V, E, F, B, H, a, c, j, d, v, e, f, b, h
SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · 8 copies · chains A, T, b, C, D, J, K, E, F, X, a, c, d, j, k, B, H, t, L, l, f, x
PHO · Pheophytin A · ligand · 4 copies · chains A, D, a, d
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 · 4 copies · chains A, D, F, X, L, T, a, d, f, x, l, t
OEX · Ca-MN4-O5 cluster · ligand · 2 copies · chains A, C, a, c
BCT · Bicarbonate ion · ligand · 2 copies · chains A, D, a, d
HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains E, F, e, f
RRX · (3R)-beta,beta-caroten-3-ol · ligand · 2 copies · chains H, X, h, x
HEC · Heme C · ligand · 2 copies · chains C, V, c, v
CA · Calcium ion · metal · 5 copies · chains B, O, b, c, o
MG · Magnesium ion · metal · 4 copies · chains F, J, K, Y, f, j, k, y
FE2 · Fe (II) ion · metal · 2 copies · chains A, D, a, d
CL · Chloride ion · ion · 4 copies · chains A, D, C, a, d, c
DMS · Dimethyl sulfoxide · additive · 133 copies · chains A, D, E, O, b, B, U, H, t, a, L, C, V, Y, F, J, I, T, o, d, i, u, h, c, v, e, f, j, l
HTG · heptyl 1-thio-beta-D-glucopyranoside · additive · 17 copies · chains B, a, o, C, D, H, U, V, A, O, b, d, u, v, c, l
LMT · Dodecyl-beta-D-maltoside · additive · 11 copies · chains A, D, O, b, B, H, E, F, J, C, I, T, Z, a, d, c, i, z, e, f, j, t

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	1197	0.86	0.87	85	CLA, BCR
2	1194	0.86	0.86	89	CLA, BCR
3	877	0.86	0.87	116	BCT, LHG, DMS
4	850	0.85	0.87	79	DMS, HEC
5	969	0.85	0.86	90	DMS, HEC

Interfaces

115 interfaces between chains.

A–D · 5446 Å² buried · 68 hydrogen bonds · protein-protein
a–d · 5439 Å² buried · 62 hydrogen bonds · protein-protein
A–C · 3289 Å² buried · 41 hydrogen bonds · protein-protein
a–c · 3267 Å² buried · 41 hydrogen bonds · protein-protein
B–D · 2929 Å² buried · 42 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 cofactor, 4 modified, 2 disulfide (heme c attachment, formylation, disulfide).

Compared structures

5H2F · Crystal structure of the PsbM-deletion mutant of photosystem II · the same entry in another collection · chain K against K, 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 Q8DIP0
Every structure of UniProt Q8DIN9
Every structure of UniProt Q8DJ43
Every structure of UniProt Q8DJZ6
Every structure of UniProt P59087
Every structure of UniProt Q9F1K9
Every structure of UniProt Q8DIN8
Every structure of UniProt P0A431
Every structure of UniProt Q8DIQ0
Every structure of UniProt Q9F1L5
Every structure of UniProt P0A386
Every structure of UniProt Q8DJI1
Every structure of UniProt Q9F1R6
Every structure of UniProt Q8DHJ2
Elsewhere: RCSB PDB 5H2F · PDBe 5H2F · UniProt P0A444 · UniProt Q8DIQ1 · UniProt Q8DIF8 · UniProt Q8CM25 · UniProt Q8DIP0 · UniProt Q8DIN9 · UniProt Q8DJ43 · UniProt Q8DJZ6 · UniProt P59087 · UniProt Q9F1K9 · UniProt Q8DIN8 · UniProt P0A431 · UniProt Q8DIQ0 · UniProt Q9F1L5 · UniProt P0A386 · UniProt Q8DJI1 · UniProt Q9F1R6 · UniProt Q8DHJ2

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