MolNFT v1 · #126807 · protein

Cryo-EM structure of the psii supercomplex from arabidopsis thaliana

5MDX · Photosystem II protein D1: “Cryo-EM structure of the psii supercomplex from arabidopsis thaliana”. Electron microscopy, 5 ligands (CLA, CHL, PHO), 20 pockets (best druggability 0.84). MolNFT v1 #126807 on GenesisL1: 3D structure…

PDB: 5MDX
Type: protein
Length: 8,271 residues
Chains: 50
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Photosystem II protein D1; Photosystem II CP47 reaction center protein; Photosystem II…
EC: 1.10.3.9
UniProt: P83755, P56777, P56778, P56761, P56779, P62095, P56780, P62100, P56782, P60129, P62109, P23321, P61839, Q39194, Q9SKI3, P56790, Q07473, Q9XF89, P04778, Q9LMQ2
Ligands: CLA, CHL, PHO, HEM, FE2
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 21 distinct chains · 53% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Photosystem II protein D1 (EC 1.10.3.9)	protein	307	55% helix, 2% strand	P83755
B, b	Photosystem II CP47 reaction center protein	protein	478	47% helix, 8% strand	P56777
C, c	Photosystem II CP43 reaction center protein	protein	433	58% helix, 4% strand	P56778
D, d	Photosystem II D2 protein (EC 1.10.3.9)	protein	336	63% helix, 1% strand	P56761
E, e	Cytochrome B559 subunit alpha	protein	72	54% helix, 0% strand	P56779
F, f	Cytochrome B559 subunit beta (psbf)	protein	29	79% helix, 0% strand	P62095
H, h	Photosystem II reaction center protein H	protein	52	63% helix, 0% strand	P56780
I, i	Photosystem II reaction center protein I	protein	35	63% helix, 0% strand	P62100
K, k	Photosystem II reaction center protein K	protein	36	58% helix, 0% strand	P56782
L, l	Photosystem II reaction center protein L	protein	36	64% helix, 0% strand	P60129
M, m	Photosystem II reaction center protein M	protein	29	90% helix, 0% strand	P62109
O, o	Oxygen-evolving enhancer protein 1-1, chloroplastic	protein	193	7% helix, 44% strand	P23321
T, t	Photosystem II reaction center protein T	protein	29	72% helix, 0% strand	P61839
W, w	Photosystem II reaction center W protein, chloroplastic	protein	46	52% helix, 2% strand	Q39194
X, x	Photosystem II reaction center protein X	protein	32	94% helix, 0% strand	Q9SKI3
Z, z	Photosystem II reaction center protein Z	protein	61	85% helix, 0% strand	P56790
a	Photosystem II protein D1 (EC 1.10.3.9)	protein	330	56% helix, 2% strand	P83755
R, r	Chlorophyll a-B binding protein CP29.1, chloroplastic	protein	188	58% helix, 4% strand	Q07473
S, s	Chlorophyll a-B binding protein CP26, chloroplastic	protein	214	45% helix, 0% strand	Q9XF89
G, N, Y, g, n, y, 1, 2, 3, 5, 6, 7	Chlorophyll a-B binding protein 1, chloroplastic	protein	219	50% helix, 1% strand	P04778
4, 8	Chlorophyll a-B binding protein, chloroplastic	protein	204	48% helix, 0% strand	Q9LMQ2

Ligands and binding sites

CLA · Chlorophyll A · ligand · 212 copies · chains A, D, C, I, W, B, H, L, M, K, X, a, d, i, w, c, b, h, l, m, x, k, R, 8, S, G, N, 5, Y, r, 4, s, g, n, 1, y, 2, 3, 6, 7
CHL · Chlorophyll B · ligand · 96 copies · chains R, b, S, G, N, Y, r, s, g, n, y, 1, 2, 3, 4, 5, 6, 7, 8
PHO · Pheophytin A · ligand · 4 copies · chains A, D, a, d
HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains E, F, e, f
FE2 · Fe (II) ion · metal · 2 copies · chains A, D, a, d

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	827	0.84	0.86	103	empty
2	1039	0.83	0.84	113	empty
3	643	0.82	0.87	88	empty
4	967	0.81	0.82	88	CLA
5	322	0.81	0.91	58	empty

Interfaces

122 interfaces between chains.

a–d · 5161 Å² buried · 38 hydrogen bonds · protein-protein
A–D · 5120 Å² buried · 35 hydrogen bonds · protein-protein
B–D · 2465 Å² buried · 23 hydrogen bonds · protein-protein
a–c · 2145 Å² buried · 11 hydrogen bonds · protein-protein
b–d · 2009 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 covalent, 2 disulfide (covalent ligand, disulfide).

Compared structures

5MDX · Cryo-EM structure of the PSII supercomplex from Arabidopsis thaliana · the same entry in another collection · chain E against E, 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 P83755
Every structure of UniProt P56777
Every structure of UniProt P56778
Every structure of UniProt P56761
Every structure of UniProt P56779
Every structure of UniProt P62095
Every structure of UniProt P56780
Every structure of UniProt P62100
Every structure of UniProt P56782
Every structure of UniProt P60129
Every structure of UniProt P62109
Every structure of UniProt P23321
Every structure of UniProt P61839
Every structure of UniProt Q39194
Every structure of UniProt Q9SKI3
Every structure of UniProt P56790
Every structure of UniProt Q07473
Every structure of UniProt Q9XF89
Every structure of UniProt P04778
Every structure of UniProt Q9LMQ2
Elsewhere: RCSB PDB 5MDX · PDBe 5MDX · UniProt P83755 · UniProt P56777 · UniProt P56778 · UniProt P56761 · UniProt P56779 · UniProt P62095 · UniProt P56780 · UniProt P62100 · UniProt P56782 · UniProt P60129 · UniProt P62109 · UniProt P23321 · UniProt P61839 · UniProt Q39194 · UniProt Q9SKI3 · UniProt P56790 · UniProt Q07473 · UniProt Q9XF89 · UniProt P04778 · UniProt Q9LMQ2

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