Research workbench

Lumbricus erythrocruorin at 3.5A resolution

Analyse Lumbricus erythrocruorin at 3.5A resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2GTL
Type: protein
Length: 2,395 residues
Chains: 15
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Extracellular globin 4; Extracellular globin 2; Extracellular globin-3; Hemoglobin chain…
UniProt: P13579, P02218, P11069, O61233, Q9GV76, Q2I743, Q2I742
Ligands: HEM, CA, ZN, CMO
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 7 distinct chains · 47% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, I	Extracellular globin 4	protein	147	73% helix, 0% strand	P13579
B, F, J	Extracellular globin 2	protein	145	76% helix, 0% strand	P02218
C, G, K	Extracellular globin-3	protein	149	74% helix, 0% strand	P11069
D, H, L	Hemoglobin chain D1	protein	140	74% helix, 0% strand	O61233
M	Hemoglobin linker chain L1	protein	217	21% helix, 33% strand	Q9GV76
N	Extracellular hemoglobin linker L2 subunit	protein	220	25% helix, 34% strand	Q2I743
O	Extracellular hemoglobin linker L3 subunit	protein	215	21% helix, 36% strand	Q2I742

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 12 copies · chains A, D, B, C, E, H, F, G, I, L, J, K
CA · Calcium ion · metal · 4 copies · chains B, M, G, N, O
ZN · Zinc ion · metal · chains N
CMO · Carbon monoxide · ion · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L

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	983	0.85	0.86	64	CMO, HEM
2	971	0.85	0.85	65	CMO, HEM
3	983	0.84	0.85	66	CMO, HEM
4	931	0.84	0.85	71	CMO, HEM
5	932	0.84	0.85	70	CMO, HEM

Interfaces

37 interfaces between chains.

M–N · 1341 Å² buried · 9 hydrogen bonds · protein-protein
N–O · 1317 Å² buried · 10 hydrogen bonds · protein-protein
E–H · 1235 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 1211 Å² buried · 9 hydrogen bonds · protein-protein
I–L · 1204 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 32 disulfide (disulfide).

Compared structures

2GTL · Lumbricus Erythrocruorin at 3.5A resolution · the same entry in another collection · chain O against O, 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 P13579
Every structure of UniProt P02218
Every structure of UniProt P11069
Every structure of UniProt O61233
Every structure of UniProt Q9GV76
Every structure of UniProt Q2I743
Every structure of UniProt Q2I742
Elsewhere: RCSB PDB 2GTL · PDBe 2GTL · UniProt P13579 · UniProt P02218 · UniProt P11069 · UniProt O61233 · UniProt Q9GV76 · UniProt Q2I743 · UniProt Q2I742

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