MolNFT v1 · #56875 · protein
Crystal structure of the cytochrome B6F complex from nostoc sp. pcc 7120
2ZT9: “Crystal structure of the cytochrome B6F complex from nostoc sp. pcc 7120”. X-ray diffraction, 7 ligands (HEM, UMQ, OPC), 10 pockets (best druggability 0.87). MolNFT v1 #56875 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2ZT9
- Type
- protein
- Length
- 959 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome B6; Cytochrome B6-F complex subunit 4; Apocytochrome F; Cytochrome B6-F…
- EC
- 1.10.99.1
- UniProt
- P0A384, Q93SX1, Q93SW9, Q93SX0, Q8YVQ2, P0A3Y1, P58246, P61048
- Ligands
- HEM, UMQ, OPC, CLA, SQD, FES, BCR
- Pockets
- 10 · best druggability 0.87
Structure
x-ray diffraction · 8 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome B6 | protein | 215 | 73% helix, 1% strand | P0A384 |
| B | Cytochrome B6-F complex subunit 4 | protein | 160 | 59% helix, 4% strand | Q93SX1 |
| C | Apocytochrome F | protein | 289 | 20% helix, 27% strand | Q93SW9 |
| D | Cytochrome B6-F complex iron-sulfur subunit 1 (EC 1.10.99.1) | protein | 166 | 23% helix, 23% strand | Q93SX0 |
| E | Cytochrome B6-F complex subunit 6 | protein | 31 | 84% helix, 0% strand | Q8YVQ2 |
| F | Cytochrome B6-F complex subunit 7 | protein | 32 | 81% helix, 0% strand | P0A3Y1 |
| G | Cytochrome B6-F complex subunit 5 | protein | 37 | 73% helix, 0% strand | P58246 |
| H | Cytochrome B6-F complex subunit 8 | protein | 29 | 83% helix, 0% strand | P61048 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, H, C
- UMQ · Undecyl-maltoside · ligand · 3 copies · chains A, B, C, D
- OPC · (7R,17E)-4-hydroxy-N,N,N,7-tetramethyl-7-[(8E)-octadec-8-enoyloxy]-10-oxo-3,5,9-trioxa-4-phosphaheptacos-17-en-1-aminium 4-oxide · ligand · 2 copies · chains A, B, C, E, F, G, H
- CLA · Chlorophyll A · ligand · chains A, B
- SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol · ligand · chains B, C, D
- FES · Fe2/s2 (inorganic) cluster · ligand · chains D
- BCR · Beta-carotene · ligand · chains A, B, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 900 | 0.87 | 0.88 | 112 | HEM, CLA |
| 2 | 781 | 0.85 | 0.87 | 101 | HEM |
| 3 | 522 | 0.85 | 0.90 | 58 | BCR, OPC |
| 4 | 216 | 0.74 | 0.89 | 38 | HEM |
| 5 | 434 | 0.64 | 0.77 | 47 | UMQ |
Interfaces
21 interfaces between chains.
- A–B · 3215 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 1289 Ų buried · 13 hydrogen bonds · protein-protein
- B–G · 978 Ų buried · 5 hydrogen bonds · protein-protein
- A–G · 836 Ų buried · 2 hydrogen bonds · protein-protein
- C–H · 808 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 cofactor (disulfide, heme attachment).
Compared structures
- 2ZT9 · Crystal Structure of the Cytochrome b6f Complex from Nostoc sp. PCC 7120 · the same entry in another collection · chain H against H, TM-score 1.00
- Q93SW9 · AlphaFold monomer V2.0 prediction for cytochrome F (Q93SW9) · a predicted model of the same protein · chain C against A, TM-score 0.98
- P0A384 · AlphaFold monomer V2.0 prediction for cytochrome B6 (P0A384) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q93SX1 · AlphaFold monomer V2.0 prediction for cytochrome B6-F complex subunit 4 (Q93SX1) · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q93SX0 · AlphaFold monomer V2.0 prediction for cytochrome B6-F complex iron- sulfur subunit 1… · a predicted model of the same protein · chain D against A, TM-score 0.93
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 P0A384
- Every structure of UniProt Q93SX1
- Every structure of UniProt Q93SW9
- Every structure of UniProt Q93SX0
- Every structure of UniProt Q8YVQ2
- Every structure of UniProt P0A3Y1
- Every structure of UniProt P58246
- Every structure of UniProt P61048
- Elsewhere: RCSB PDB 2ZT9 · PDBe 2ZT9 · UniProt P0A384 · UniProt Q93SX1 · UniProt Q93SW9 · UniProt Q93SX0 · UniProt Q8YVQ2 · UniProt P0A3Y1 · UniProt P58246 · UniProt P61048
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