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
- 5ZGH
- Type
- protein
- Length
- 2,757 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LHCR1; LHCR2; LHCR3; Psaa; Psab; Psac; Psad; Psae; Psaf; Psai; Psaj; Psak; Psal; Psam…
- EC
- 1.97.1.12
- UniProt
- M1VKK5, M1UU36, Q85FY7, Q85FY6, Q85G47, Q85FY0, Q85FZ1, Q85FS9, Q85FQ6, Q85FS8, Q85G51, Q85FP8, Q85G73, M1VFJ4
- Ligands
- CLA, BCR, ZEX, SF4, PQN, LHG, 1DO, CL0, DGD, 3XQ, BGC
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 15 distinct chains · 50% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | LHCR1 | protein | 169 | 41% helix, 0% strand | M1VKK5 |
| 2 | LHCR2 | protein | 175 | 48% helix, 0% strand | M1UU36 |
| 3 | LHCR3 | protein | 170 | 48% helix, 0% strand | — |
| A | Psaa (EC 1.97.1.12) | protein | 741 | 57% helix, 3% strand | Q85FY7 |
| B | Psab (EC 1.97.1.12) | protein | 731 | 55% helix, 2% strand | Q85FY6 |
| C | Psac (EC 1.97.1.12) | protein | 80 | 16% helix, 20% strand | Q85G47 |
| D | Psad | protein | 119 | 13% helix, 18% strand | Q85FY0 |
| E | Psae | protein | 61 | 0% helix, 28% strand | Q85FZ1 |
| F | Psaf | protein | 154 | 60% helix, 4% strand | Q85FS9 |
| I | Psai | protein | 31 | 68% helix, 0% strand | Q85FQ6 |
| J | Psaj | protein | 38 | 58% helix, 0% strand | Q85FS8 |
| K | Psak | protein | 59 | 64% helix, 0% strand | Q85G51 |
| L | Psal | protein | 119 | 61% helix, 0% strand | Q85FP8 |
| M | Psam | protein | 27 | 78% helix, 0% strand | Q85G73 |
| O | Psao | protein | 83 | 45% helix, 0% strand | M1VFJ4 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 133 copies · chains 1, 2, F, J, 3, A, K, B, O, L, I, M
- BCR · Beta-carotene · ligand · 21 copies · chains A, O, B, K, F, J, I, 3, L
- 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 · 15 copies · chains 1, 2, 3, K
- 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
- 1DO · 1-dodecanol · ligand · chains 3, 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
- BGC · beta-D-glucopyranose · sugar · chains 3, A
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 | 593 | 0.81 | 0.85 | 61 | CL0, CLA |
| 2 | 464 | 0.79 | 0.86 | 41 | CLA |
| 3 | 769 | 0.78 | 0.82 | 64 | DGD |
| 4 | 686 | 0.71 | 0.78 | 68 | CLA |
| 5 | 536 | 0.69 | 0.78 | 68 | CLA, LHG |
Interfaces
34 interfaces between chains.
- A–B · 3512 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 1520 Ų buried · 21 hydrogen bonds · protein-protein
- B–F · 1144 Ų buried · 12 hydrogen bonds · protein-protein
- A–F · 1134 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 870 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5ZGH · Cryo-EM structure of the red algal PSI-LHCR · the same entry in another collection · chain O against O, 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 M1VKK5
- Every structure of UniProt M1UU36
- 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
- Elsewhere: RCSB PDB 5ZGH · PDBe 5ZGH · UniProt M1VKK5 · UniProt M1UU36 · UniProt Q85FY7 · UniProt Q85FY6 · UniProt Q85G47 · UniProt Q85FY0 · UniProt Q85FZ1 · UniProt Q85FS9 · UniProt Q85FQ6 · UniProt Q85FS8 · UniProt Q85G51 · UniProt Q85FP8 · UniProt Q85G73 · UniProt M1VFJ4
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