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Crystal structure of cytochrome C554 from vibrio parahaemolyticus strain RIMD2210633

Analyse Crystal structure of cytochrome C554 from vibrio parahaemolyticus strain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2ZZS
Type: protein
Length: 2,589 residues
Chains: 32
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome C554
UniProt: Q87MF5
Ligands: HEC
Pockets: 20 · best druggability 0.90

Structure

x-ray diffraction · 3 distinct chains · 53% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, 1, 2, 3, 4, 5	Cytochrome C554	protein	81	54% helix, 1% strand	Q87MF5
M	Cytochrome C554	protein	80	58% helix, 1% strand	Q87MF5
6	Cytochrome C554	protein	79	47% helix, 0% strand	Q87MF5

Ligands and binding sites

HEC · Heme C · ligand · 32 copies · chains A, B, T, M, C, D, F, E, O, G, H, Y, I, J, U, K, L, N, P, Q, R, V, S, W, X, Z, 1, 2, 3, 4, 5, 6
GOL · Glycerol · additive · 4 copies · chains C, D, E, F, O, P, R

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

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	942	0.90	0.92	130	HEC
2	722	0.90	0.94	119	HEC
3	1043	0.90	0.91	141	HEC
4	1074	0.89	0.91	141	HEC
5	1075	0.88	0.89	133	HEC

Interfaces

72 interfaces between chains.

K–L · 766 Å² buried · 16 hydrogen bonds · protein-protein
Q–R · 745 Å² buried · 12 hydrogen bonds · protein-protein
W–X · 717 Å² buried · 14 hydrogen bonds · protein-protein
1–2 · 713 Å² buried · 16 hydrogen bonds · protein-protein
M–N · 711 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 63 cofactor (heme c attachment).

Compared structures

2ZZS · Crystal structure of cytochrome c554 from Vibrio parahaemolyticus strain RIMD2210633 · 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 Q87MF5
Elsewhere: RCSB PDB 2ZZS · PDBe 2ZZS · UniProt Q87MF5

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