MolNFT v1 · #152422 · protein
Structure of psi-lhci
6IGZ · Psaa: “Structure of psi-lhci”. Electron microscopy, 9 ligands (CLA, 8CT, CHL), 20 pockets (best druggability 0.78). MolNFT v1 #152422 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6IGZ
- Type
- protein
- Length
- 4,518 residues
- Chains
- 23
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Psaa; Psab; Psac; Psad; Psae; Psaf; Psag; Psah; Psai; Psaj; Psak; Psal; Lhca-a; Lhca-C…
- UniProt
- A0A0D6E2L8
- Ligands
- CLA, 8CT, CHL, XAT, LHG, SF4, LMG, PQN, DGD
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 23 distinct chains · 51% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Psaa | protein | 740 | 58% helix, 3% strand | — |
| B | Psab | protein | 733 | 59% helix, 2% strand | — |
| C | Psac | protein | 80 | 6% helix, 15% strand | — |
| D | Psad | protein | 142 | 17% helix, 20% strand | — |
| E | Psae | protein | 61 | 0% helix, 34% strand | — |
| F | Psaf | protein | 163 | 62% helix, 4% strand | — |
| G | Psag | protein | 92 | 57% helix, 2% strand | — |
| H | Psah | protein | 88 | 30% helix, 1% strand | — |
| I | Psai | protein | 32 | 72% helix, 0% strand | — |
| J | Psaj | protein | 41 | 71% helix, 0% strand | — |
| K | Psak | protein | 80 | 49% helix, 0% strand | — |
| L | Psal | protein | 155 | 55% helix, 1% strand | — |
| 1 | Lhca-a | protein | 193 | 55% helix, 0% strand | — |
| 2 | Lhca-C | protein | 212 | 52% helix, 0% strand | — |
| 3 | Lhca-D | protein | 226 | 50% helix, 0% strand | — |
| 4 | Lhca-B | protein | 207 | 48% helix, 0% strand | — |
| 6 | Lhca-G | protein | 229 | 40% helix, 2% strand | — |
| 5 | Lhca-a | protein | 195 | 53% helix, 1% strand | — |
| 7 | Lhca-H | protein | 228 | 42% helix, 1% strand | — |
| 8 | Lhca-B | protein | 205 | 51% helix, 0% strand | — |
| 9 | Lhca-I | protein | 183 | 53% helix, 0% strand | — |
| 0 | Lhca-J | protein | 202 | 52% helix, 0% strand | — |
| M | Photosystem I reaction center subunit XII | protein | 31 | 87% helix, 0% strand | A0A0D6E2L8 |
Ligands and binding sites
- CLA · Chlorophyll A · ligand · 218 copies · chains A, B, F, J, 3, K, L, I, M, G, 9, H, 1, 4, 2, 6, 7, 8, 5, 0
- 8CT · (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene · ligand · 34 copies · chains A, B, K, F, G, 9, H, I, L, J, 1, 2, 3, 4, 6, 5, 7, 8
- CHL · Chlorophyll B · ligand · 26 copies · chains 1, 2, 3, 4, 6, 7, 8, 5, 9, 0
- XAT · (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-tetrahydro-beta,beta-carotene-3,3'-diol · ligand · 20 copies · chains 1, 2, 3, 4, 6, 5, 7, 8, 9, 0
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 11 copies · chains A, B, 1, 4, 2, 3, 6, 7, 5, 8, 9, 0
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A, B, C
- LMG · 1,2-distearoyl-monogalactosyl-diglyceride · ligand · 3 copies · chains 2, 4, 5, 8
- PQN · Phylloquinone · ligand · 2 copies · chains A, J, B
- DGD · Digalactosyl diacyl glycerol (dgdg) · ligand · chains B, C
- HTG · heptyl 1-thio-beta-D-glucopyranoside · additive · 2 copies · chains A, F, 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 946 | 0.78 | 0.80 | 62 | DGD |
| 2 | 794 | 0.78 | 0.82 | 86 | empty |
| 3 | 784 | 0.73 | 0.78 | 91 | CLA |
| 4 | 806 | 0.72 | 0.77 | 83 | CLA |
| 5 | 721 | 0.72 | 0.78 | 80 | CLA |
Interfaces
54 interfaces between chains.
- A–B · 3455 Ų buried · 37 hydrogen bonds · protein-protein
- H–L · 1953 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1674 Ų buried · 25 hydrogen bonds · protein-protein
- B–G · 1182 Ų buried · 21 hydrogen bonds · protein-protein
- A–F · 1084 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 6IGZ · Structure of PSI-LHCI · the same entry in another collection · chain B against B, 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 A0A0D6E2L8
- Elsewhere: RCSB PDB 6IGZ · PDBe 6IGZ · UniProt A0A0D6E2L8
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