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Crystal structure of rhodospirillum rubrum RRU_A0973 E34A variant

Analyse Crystal structure of rhodospirillum rubrum RRU_A0973 E34A variant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6SV1
Type: protein
Length: 2,696 residues
Chains: 30
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Encapsulated ferritin
UniProt: Q2RVS1
Ligands: FE, CA
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 7 distinct chains · 78% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F, W, c	Encapsulated ferritin	protein	90	81% helix, 0% strand	Q2RVS1
B, C, D, E, G, I, K, S, T, V, X, Z, a	Encapsulated ferritin	protein	91	76% helix, 0% strand	Q2RVS1
H	Encapsulated ferritin	protein	89	78% helix, 0% strand	Q2RVS1
J, N, Q, U	Encapsulated ferritin	protein	89	78% helix, 0% strand	Q2RVS1
L	Encapsulated ferritin	protein	84	82% helix, 0% strand	Q2RVS1
M, O, R	Encapsulated ferritin	protein	88	78% helix, 0% strand	Q2RVS1
P, Y, b, d	Encapsulated ferritin	protein	90	77% helix, 0% strand	Q2RVS1

Ligands and binding sites

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 · 18 copies · chains B, C, D, Q, F, H, I, J, A, K, T, L, S, V, W, X, Y, E, 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, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1095	0.79	0.81	106	CA
2	1034	0.75	0.78	76	empty
3	970	0.74	0.78	93	CA
4	474	0.66	0.78	105	empty
5	325	0.59	0.77	58	empty

Interfaces

78 interfaces between chains.

Q–R · 2560 Å² buried · 49 hydrogen bonds · protein-protein
I–J · 2557 Å² buried · 48 hydrogen bonds · protein-protein
G–H · 2554 Å² buried · 49 hydrogen bonds · protein-protein
a–b · 2550 Å² buried · 48 hydrogen bonds · protein-protein
c–d · 2547 Å² buried · 43 hydrogen bonds · protein-protein

Compared structures

6SV1 · Crystal structure of Rhodospirillum rubrum Rru_A0973 E34A variant · the same entry in another collection · chain B against B, 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 Q2RVS1
Elsewhere: RCSB PDB 6SV1 · PDBe 6SV1 · UniProt Q2RVS1

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