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Crystal structure of cytochrome B6F complex with dbmib from M. laminosus

Analyse Crystal structure of cytochrome B6F complex with dbmib from M. laminosus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2D2C
Type: protein
Length: 1,828 residues
Chains: 16
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: P83791, P83792, P83793, P83794, P83795, P83796, P83797, P83798
Ligands: HEM, OPC, HEC, BNT, CLA, FES, BCR
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 8 distinct chains · 33% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, N	Cytochrome B6	protein	202	57% helix, 0% strand	P83791
B, O	Cytochrome B6-F complex subunit 4	protein	137	39% helix, 0% strand	P83792
C, P	Apocytochrome F	protein	286	15% helix, 14% strand	P83793
D, Q	Cytochrome B6-F complex iron-sulfur subunit (EC 1.10.99.1)	protein	168	14% helix, 8% strand	P83794
E, R	Cytochrome B6-F complex subunit VI	protein	32	47% helix, 0% strand	P83795
F, S	Cytochrome B6-F complex subunit VII	protein	35	66% helix, 0% strand	P83796
G, T	Cytochrome B6-F complex subunit V	protein	27	33% helix, 0% strand	P83797
H, U	Cytochrome B6-F complex subunit VIII	protein	27	74% helix, 0% strand	P83798

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 6 copies · chains A, B, N, C, O, 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 B, D, C, N, O, Q, P
HEC · Heme C · ligand · 2 copies · chains A, B, N, O, T
BNT · 2,5-dibromo-3-isopropyl-6-methylbenzo-1,4-quinone · ligand · 2 copies · chains A, B, C, N, O, P
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	804	0.88	0.91	85	HEM, BNT
2	716	0.87	0.90	82	BCR
3	946	0.86	0.87	93	HEM, BNT
4	543	0.86	0.91	61	BCR
5	479	0.81	0.87	57	HEM, CLA

Interfaces

49 interfaces between chains.

N–O · 2697 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 2656 Å² buried · 22 hydrogen bonds · protein-protein
A–N · 1216 Å² buried · 4 hydrogen bonds · protein-protein
O–P · 983 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 898 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

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

Compared structures

2D2C · Crystal Structure Of Cytochrome B6F Complex with DBMIB 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 2D2C · PDBe 2D2C · UniProt P83791 · UniProt P83792 · UniProt P83793 · UniProt P83794 · UniProt P83795 · UniProt P83796 · UniProt P83797 · UniProt P83798

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