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Crystal structure of rhodospirillum rubrum RRU_A0973

Analyse Crystal structure of rhodospirillum rubrum RRU_A0973 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5DA5
Type: protein
Length: 2,703 residues
Chains: 30
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RRU_A0973
UniProt: Q2RVS1
Ligands: GOA, FE, CA
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 6 distinct chains · 79% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, F, G, H, I, J, K, L, N, T, U, a, d	RRU_A0973	protein	91	79% helix, 0% strand	Q2RVS1
C, E, M, O, Q, R, V, W	RRU_A0973	protein	90	78% helix, 0% strand	Q2RVS1
P	RRU_A0973	protein	90	80% helix, 0% strand	Q2RVS1
S, X, Y, Z	RRU_A0973	protein	89	78% helix, 0% strand	Q2RVS1
b	RRU_A0973	protein	88	80% helix, 0% strand	Q2RVS1
c	RRU_A0973	protein	84	82% helix, 0% strand	Q2RVS1

Ligands and binding sites

GOA · Glycolic acid · ligand · 16 copies · chains A, J, B, C, D, E, F, H, G, I, K, T, L, M, N, O, P, R, Q, S, U, d, V, W, X, Y, Z, b, a, c
FE · Fe (III) ion · metal · 30 copies · chains A, J, B, C, D, E, F, H, G, I, K, T, L, M, N, O, P, R, Q, S, U, d, V, W, X, Y, Z, b, a, c
CA · Calcium ion · metal · 28 copies · chains A, J, B, C, D, E, F, H, G, I, K, T, L, M, N, O, P, R, Q, S, U, d, V, W, X, Y, Z, b, a, c

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1107	0.80	0.81	102	CA
2	1150	0.74	0.78	71	empty
3	761	0.67	0.75	68	CA
4	194	0.52	0.78	31	empty
5	187	0.51	0.77	36	empty

Interfaces

77 interfaces between chains.

E–F · 2593 Å² buried · 43 hydrogen bonds · protein-protein
W–X · 2589 Å² buried · 45 hydrogen bonds · protein-protein
Q–R · 2586 Å² buried · 43 hydrogen bonds · protein-protein
U–V · 2584 Å² buried · 48 hydrogen bonds · protein-protein
C–D · 2579 Å² buried · 45 hydrogen bonds · protein-protein

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Every structure of UniProt Q2RVS1
Elsewhere: RCSB PDB 5DA5 · PDBe 5DA5 · UniProt Q2RVS1

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