Research workbench
Cryo-EM structure of the red algal psi-lhcr
Analyse Cryo-EM structure of the red algal psi-lhcr in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZGB
- Type
- protein
- Length
- 3,102 residues
- Chains
- 17
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Psaa; Psab; Psac; Psad; Psae; Psaf; Psai; Psaj; Psak; Psal; Psam; Psao; LHCR1; LHCR2…
- EC
- 1.97.1.12
- UniProt
- Q85FY7, Q85FY6, Q85G47, Q85FY0, Q85FZ1, Q85FS9, Q85FQ6, Q85FS8, Q85G51, Q85FP8, Q85G73, M1VFJ4, M1VKK5, M1UU36
- Ligands
- CLA, ZEX, BCR, SF4, PQN, LHG, CL0, DGD, 3XQ, 1DO, BGC
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 16 distinct chains · 50% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Psaa (EC 1.97.1.12) | protein | 741 | 57% helix, 3% strand | Q85FY7 |
| B | Psab (EC 1.97.1.12) | protein | 731 | 56% helix, 2% strand | Q85FY6 |
| C | Psac (EC 1.97.1.12) | protein | 80 | 20% helix, 20% strand | Q85G47 |
| D | Psad | protein | 119 | 16% helix, 17% strand | Q85FY0 |
| E | Psae | protein | 61 | 0% helix, 30% strand | Q85FZ1 |
| F | Psaf | protein | 154 | 58% helix, 3% strand | Q85FS9 |
| I | Psai | protein | 31 | 74% helix, 0% strand | Q85FQ6 |
| J | Psaj | protein | 38 | 66% helix, 0% strand | Q85FS8 |
| K | Psak | protein | 59 | 68% helix, 0% strand | Q85G51 |
| L | Psal | protein | 119 | 62% helix, 0% strand | Q85FP8 |
| M | Psam | protein | 27 | 78% helix, 0% strand | Q85G73 |
| O | Psao | protein | 83 | 47% helix, 0% strand | M1VFJ4 |
| 1 | LHCR1 | protein | 169 | 38% helix, 0% strand | M1VKK5 |
| 2, 5 | LHCR2 | protein | 175 | 47% helix, 0% strand | M1UU36 |
| 3 | LHCR3 | protein | 170 | 47% helix, 0% strand | — |
| 4 | LHCR1 | protein | 170 | 38% helix, 0% strand | M1VKK5 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 157 copies · chains A, J, B, 2, 3, K, O, L, I, F, M, 5, 1, 4
- ZEX · (1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol · ligand · 25 copies · chains 1, 2, 3, K, 4, 5, M, I
- BCR · Beta-carotene · ligand · 21 copies · chains A, B, F, J, I, K, 3, L, O
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A, B, C
- PQN · Phylloquinone · ligand · 2 copies · chains A, J, B
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 2 copies · chains A
- CL0 · Chlorophyll A isomer · ligand · chains A, B
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · chains B, C
- 3XQ · (2S)-2,3-dihydroxypropyl octadecanoate · ligand · chains B, F, J
- 1DO · 1-dodecanol · ligand · chains A, 3
- BGC · beta-D-glucopyranose · sugar · chains A, 3
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.86 | 0.86 | 87 | CL0, CLA |
| 2 | 944 | 0.80 | 0.81 | 84 | CLA, DGD |
| 3 | 888 | 0.73 | 0.77 | 98 | CLA, LHG |
| 4 | 50 | 0.72 | 0.99 | 21 | SF4 |
| 5 | 800 | 0.71 | 0.76 | 85 | CLA, 3XQ |
Interfaces
41 interfaces between chains.
- A–B · 3496 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 1477 Ų buried · 20 hydrogen bonds · protein-protein
- B–F · 1163 Ų buried · 12 hydrogen bonds · protein-protein
- A–F · 1147 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 862 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5ZGB · Cryo-EM structure of the red algal PSI-LHCR · the same entry in another collection · chain 5 against 5, 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 Q85FY7
- Every structure of UniProt Q85FY6
- Every structure of UniProt Q85G47
- Every structure of UniProt Q85FY0
- Every structure of UniProt Q85FZ1
- Every structure of UniProt Q85FS9
- Every structure of UniProt Q85FQ6
- Every structure of UniProt Q85FS8
- Every structure of UniProt Q85G51
- Every structure of UniProt Q85FP8
- Every structure of UniProt Q85G73
- Every structure of UniProt M1VFJ4
- Every structure of UniProt M1VKK5
- Every structure of UniProt M1UU36
- Elsewhere: RCSB PDB 5ZGB · PDBe 5ZGB · UniProt Q85FY7 · UniProt Q85FY6 · UniProt Q85G47 · UniProt Q85FY0 · UniProt Q85FZ1 · UniProt Q85FS9 · UniProt Q85FQ6 · UniProt Q85FS8 · UniProt Q85G51 · UniProt Q85FP8 · UniProt Q85G73 · UniProt M1VFJ4 · UniProt M1VKK5 · UniProt M1UU36
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