MolNFT v1 · #125414 · protein

Crystal structure of rhodospirillum rubrum RRU_A0973 mutant E32A

5L89: “Crystal structure of rhodospirillum rubrum RRU_A0973 mutant E32A”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.82). MolNFT v1 #125414 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5L89
Type: protein
Length: 2,684 residues
Chains: 30
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RRU_A0973
UniProt: Q2RVS1
Ligands: CA
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 8 distinct chains · 77% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, F, G, L, N, P, U	RRU_A0973	protein	91	73% helix, 0% strand	Q2RVS1
B, C, E, I, O, R, W, d	RRU_A0973	protein	90	73% helix, 0% strand	Q2RVS1
H, T, a	RRU_A0973	protein	90	78% helix, 0% strand	Q2RVS1
J, K, M, Q, S	RRU_A0973	protein	89	78% helix, 0% strand	Q2RVS1
V	RRU_A0973	protein	89	78% helix, 0% strand	Q2RVS1
X, Z, b	RRU_A0973	protein	88	75% helix, 0% strand	Q2RVS1
Y	RRU_A0973	protein	85	82% helix, 0% strand	Q2RVS1
c	RRU_A0973	protein	83	83% helix, 0% strand	Q2RVS1

Ligands and binding sites

CA · Calcium ion · metal · 9 copies · chains C, D, G, I, L, M, N, P, R, Q, S, U, V, W, d

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

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	999	0.82	0.83	108	empty
2	976	0.77	0.79	71	empty
3	50	0.67	0.96	18	CA
4	709	0.65	0.75	65	empty
5	65	0.65	0.93	18	CA

Interfaces

76 interfaces between chains.

Q–R · 2567 Å² buried · 44 hydrogen bonds · protein-protein
M–N · 2563 Å² buried · 49 hydrogen bonds · protein-protein
C–D · 2561 Å² buried · 44 hydrogen bonds · protein-protein
E–F · 2557 Å² buried · 46 hydrogen bonds · protein-protein
K–L · 2554 Å² buried · 47 hydrogen bonds · protein-protein

Compared structures

5L89 · Crystal structure of Rhodospirillum rubrum Rru_A0973 mutant E32A · 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 5L89 · PDBe 5L89 · UniProt Q2RVS1

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