MolNFT v1 · #25084 · protein

Crystal structure of cytochrome B6F complex from M.LAMINOSUS

1VF5: “Crystal structure of cytochrome B6F complex from M.LAMINOSUS”. X-ray diffraction, 7 ligands (HEM, OPC, TDS), 20 pockets (best druggability 0.86). MolNFT v1 #25084 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1VF5
Type: protein
Length: 1,824 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome B6; Subunit IV; Cytochrome F; Rieske iron-sulfur protein; Protein pet L…
UniProt: P83791, P83792, P83793, P83794, P83795, P83796, P83797, P83798
Ligands: HEM, OPC, TDS, PL9, CLA, FES, BCR
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 10 distinct chains · 41% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, N	Cytochrome B6	protein	202	66% helix, 0% strand	P83791
B, O	Subunit IV	protein	138	43% helix, 1% strand	P83792
C, P	Cytochrome F	protein	286	16% helix, 21% strand	P83793
D, Q	Rieske iron-sulfur protein	protein	168	15% helix, 10% strand	P83794
E, R	Protein pet L	protein	32	69% helix, 0% strand	P83795
F	Protein pet M	protein	33	79% helix, 0% strand	P83796
G	Protein pet G	protein	23	78% helix, 0% strand	P83797
H, U	Protein pet N	protein	27	85% helix, 0% strand	P83798
S	Protein pet M	protein	35	74% helix, 0% strand	P83796
T	Protein pet G	protein	27	67% helix, 0% strand	P83797

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains A, N, B, C, O, T, P
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 · 4 copies · chains A, B, C, D, N, Q, O, P
TDS · 8-hydroxy-5,7-dimethoxy-3-methyl-2-tridecyl-4H-chromen-4-one · ligand · 2 copies · chains A, B, N, O
PL9 · 2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2, 6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone · ligand · 2 copies · chains A, D, N, O, Q
CLA · Chlorophyll A · ligand · 2 copies · chains A, B, N, O
FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains D, Q
BCR · Beta-carotene · ligand · 2 copies · chains A, B, E, F, G, N, O, R, S, T

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	620	0.86	0.90	61	BCR
2	777	0.85	0.88	93	HEM, CLA
3	608	0.85	0.89	57	BCR
4	618	0.85	0.89	68	HEM
5	588	0.84	0.89	60	HEM

Interfaces

49 interfaces between chains.

A–B · 2839 Å² buried · 28 hydrogen bonds · protein-protein
N–O · 2742 Å² buried · 22 hydrogen bonds · protein-protein
A–N · 1388 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 1019 Å² buried · 6 hydrogen bonds · protein-protein
O–P · 934 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 cofactor, 2 disulfide (heme attachment, disulfide).

Compared structures

1VF5 · Crystal Structure of Cytochrome b6f Complex from M.laminosus · the same entry in another collection · chain P against P, 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 P83791
Every structure of UniProt P83792
Every structure of UniProt P83793
Every structure of UniProt P83794
Every structure of UniProt P83795
Every structure of UniProt P83796
Every structure of UniProt P83797
Every structure of UniProt P83798
Elsewhere: RCSB PDB 1VF5 · PDBe 1VF5 · UniProt P83791 · UniProt P83792 · UniProt P83793 · UniProt P83794 · UniProt P83795 · UniProt P83796 · UniProt P83797 · UniProt P83798

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