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Crystal structure analysis of superoxide dismutase from trichoderma reesei

Analyse Crystal structure analysis of superoxide dismutase from trichoderma reesei in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6DQY
Type: protein
Length: 4,983 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Superoxide dismutase
EC: 1.15.1.1
UniProt: G0RQS7
Ligands: MN
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 6 distinct chains · 58% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, E, F, G, H, K, M, O, P, W, X	Superoxide dismutase (EC 1.15.1.1)	protein	208	59% helix, 12% strand	G0RQS7
D, N, S, T, U, V	Superoxide dismutase (EC 1.15.1.1)	protein	207	59% helix, 12% strand	G0RQS7
I, J	Superoxide dismutase (EC 1.15.1.1)	protein	211	58% helix, 12% strand	G0RQS7
L	Superoxide dismutase (EC 1.15.1.1)	protein	210	59% helix, 12% strand	G0RQS7
Q	Superoxide dismutase (EC 1.15.1.1)	protein	206	59% helix, 12% strand	G0RQS7
R	Superoxide dismutase (EC 1.15.1.1)	protein	199	57% helix, 13% strand	G0RQS7

Ligands and binding sites

MN · Manganese (II) ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X

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	1128	0.83	0.84	102	empty
2	1100	0.70	0.74	127	empty
3	743	0.69	0.76	62	empty
4	639	0.61	0.73	94	empty
5	549	0.61	0.74	62	empty

Interfaces

48 interfaces between chains.

C–O · 1092 Å² buried · 6 hydrogen bonds · protein-protein
K–M · 1085 Å² buried · 4 hydrogen bonds · protein-protein
E–P · 1084 Å² buried · 5 hydrogen bonds · protein-protein
B–G · 1082 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 1071 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6DQY · Crystal Structure analysis of Superoxide Dismutase from Trichoderma reesei · the same entry in another collection · chain A against A, 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 G0RQS7
Elsewhere: RCSB PDB 6DQY · PDBe 6DQY · UniProt G0RQS7

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