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Structure of rc-LH1-pufx from rhodobacter veldkampii

Analyse Structure of rc-LH1-pufx from rhodobacter veldkampii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7DDQ
Type: protein
Length: 2,354 residues
Chains: 34
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antenna pigment protein alpha chain; Antenna pigment protein beta chain; Pufx…
UniProt: A0A2T4JIR4, A0A2T4JIL7, A0A2T4JIP3, A0A2T4JIS6, A0A2T4JIN0, A0A2T4JIP4
Ligands: BCL, SPO, U10, BPH, 3PE, FE
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 9 distinct chains · 55% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
o, t, r, e, b, k, f, s, n, i, j, g, d	Antenna pigment protein alpha chain	protein	53	75% helix, 0% strand	A0A2T4JIR4
N, S, O, D, A, J, E, R, K, G, I, F, B	Antenna pigment protein beta chain	protein	44	73% helix, 0% strand	A0A2T4JIL7
a	Antenna pigment protein alpha chain	protein	44	77% helix, 0% strand	A0A2T4JIR4
U, T	Antenna pigment protein beta chain	protein	43	72% helix, 0% strand	A0A2T4JIL7
u	Antenna pigment protein alpha chain	protein	52	77% helix, 0% strand	A0A2T4JIR4
X	Pufx	protein	81	48% helix, 0% strand	A0A2T4JIP3
L	Photosynthetic reaction center L subunit	protein	275	64% helix, 4% strand	A0A2T4JIS6
M	Reaction center protein M chain	protein	305	60% helix, 4% strand	A0A2T4JIN0
H	Photosynthetic reaction center subunit H	protein	250	24% helix, 24% strand	A0A2T4JIP4

Ligands and binding sites

BCL · Bacteriochlorophyll A · ligand · 34 copies · chains o, N, O, n, t, S, T, s, u, r, R, a, A, X, e, D, E, d, b, L, B, k, J, K, j, f, U, i, G, I, g, M, F
SPO · Spheroidene · ligand · 15 copies · chains o, N, k, n, t, u, T, s, r, O, R, e, D, b, d, B, K, j, f, E, a, A, X, S, J, i, M, I, g, G, F
U10 · Ubiquinone-10 · ligand · 6 copies · chains a, b, A, L, M, r, s
BPH · Bacteriopheophytin A · ligand · 3 copies · chains L, M, n
3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 3 copies · chains L, M, H, g, b, d
FE · Fe (III) 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	844	0.85	0.86	96	U10
2	947	0.83	0.84	90	BCL
3	741	0.82	0.85	72	SPO
4	167	0.78	0.95	51	empty
5	486	0.72	0.81	53	SPO

Interfaces

98 interfaces between chains.

L–M · 4551 Å² buried · 57 hydrogen bonds · protein-protein
M–H · 2955 Å² buried · 37 hydrogen bonds · protein-protein
L–H · 1632 Å² buried · 15 hydrogen bonds · protein-protein
X–L · 1569 Å² buried · 24 hydrogen bonds · protein-protein
S–s · 785 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

7DDQ · Structure of RC-LH1-PufX from Rhodobacter veldkampii · the same entry in another collection · chain t against t, 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 A0A2T4JIR4
Every structure of UniProt A0A2T4JIL7
Every structure of UniProt A0A2T4JIP3
Every structure of UniProt A0A2T4JIS6
Every structure of UniProt A0A2T4JIN0
Every structure of UniProt A0A2T4JIP4
Elsewhere: RCSB PDB 7DDQ · PDBe 7DDQ · UniProt A0A2T4JIR4 · UniProt A0A2T4JIL7 · UniProt A0A2T4JIP3 · UniProt A0A2T4JIS6 · UniProt A0A2T4JIN0 · UniProt A0A2T4JIP4

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