Research workbench
Crystal structure of the cytochrome B6F complex from nostoc sp. pcc 7120
Analyse Crystal structure of the cytochrome B6F complex from nostoc sp. pcc 7120 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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