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Rba sphaeroides pufy-ko rc-LH1 monomer

Analyse Rba sphaeroides pufy-ko rc-LH1 monomer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7VNM
Type: protein
Length: 2,112 residues
Chains: 30
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Reaction center protein L chain; Reaction center protein M chain; Reaction center protein…
UniProt: Q3J1A5, Q3J1A6, Q3J170, Q3J1A4, Q3J1A3, P13402
Ligands: BCL, SPO, PC1, BPH, U10, CDL, FE2
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · 13 distinct chains · 60% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Reaction center protein L chain	protein	281	62% helix, 4% strand	Q3J1A5
M	Reaction center protein M chain	protein	305	65% helix, 3% strand	Q3J1A6
H	Reaction center protein H chain	protein	247	24% helix, 23% strand	Q3J170
A, D, F, I, K, O, Q, S, U, W, 9	Light-harvesting protein B-875 alpha chain	protein	54	74% helix, 0% strand	Q3J1A4
B	Light-harvesting protein B-875 beta chain	protein	45	71% helix, 0% strand	Q3J1A3
E, G, J, N, P, R, T	Light-harvesting protein B-875 beta chain	protein	43	74% helix, 0% strand	Q3J1A3
V	Light-harvesting protein B-875 beta chain	protein	40	80% helix, 0% strand	Q3J1A3
C	Light-harvesting protein B-875 beta chain	protein	38	84% helix, 0% strand	Q3J1A3
7	Light-harvesting protein B-875 alpha chain	protein	46	67% helix, 0% strand	Q3J1A4
8, 0	Light-harvesting protein B-875 beta chain	protein	44	73% helix, 0% strand	Q3J1A3
X	Intrinsic membrane protein pufx	protein	52	71% helix, 0% strand	P13402
1	Light-harvesting protein B-875 alpha chain	protein	43	77% helix, 0% strand	Q3J1A4
2	Light-harvesting protein B-875 beta chain	protein	32	84% helix, 0% strand	Q3J1A3

Ligands and binding sites

BCL · Bacteriochlorophyll A · ligand · 30 copies · chains L, M, A, B, 9, 0, D, E, F, G, I, J, K, N, O, P, Q, R, S, T, U, V, W, C, 7, 8, X, 1, 2
SPO · Spheroidene · ligand · 22 copies · chains M, O, Q, A, B, D, 9, 0, E, F, G, I, J, K, N, P, R, S, T, U, V, W, 7, 8, X
PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 7 copies · chains L, D, M, H, A, 9, 7, X
BPH · Bacteriopheophytin A · ligand · 2 copies · chains L, M
U10 · Ubiquinone-10 · ligand · 2 copies · chains L, M, 9
CDL · Cardiolipin · ligand · chains L, M, H, I, K
FE2 · Fe (II) ion · metal · chains L, M

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	665	0.82	0.86	68	empty
2	875	0.82	0.84	82	BCL
3	559	0.80	0.85	56	SPO
4	801	0.79	0.82	80	SPO, PC1
5	571	0.79	0.84	66	empty

Interfaces

86 interfaces between chains.

L–M · 4715 Å² buried · 60 hydrogen bonds · protein-protein
M–H · 2915 Å² buried · 34 hydrogen bonds · protein-protein
L–H · 1632 Å² buried · 13 hydrogen bonds · protein-protein
L–X · 886 Å² buried · 6 hydrogen bonds · protein-protein
7–8 · 820 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

7VNM · Rba sphaeroides PufY-KO RC-LH1 monomer · the same entry in another collection · chain I against I, 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 Q3J1A5
Every structure of UniProt Q3J1A6
Every structure of UniProt Q3J170
Every structure of UniProt Q3J1A4
Every structure of UniProt Q3J1A3
Every structure of UniProt P13402
Elsewhere: RCSB PDB 7VNM · PDBe 7VNM · UniProt Q3J1A5 · UniProt Q3J1A6 · UniProt Q3J170 · UniProt Q3J1A4 · UniProt Q3J1A3 · UniProt P13402

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