SMTL ID : 7ded.1

Mevo lectin complex with mannoheptose (Man7)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.23 Å

Oligo State

homo-heptamer

Ligands

3 x MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose

MAN-MAN-MAN-MAN-MAN-MAN.1: 8 residues within 4Å: Chain D: G.13, G.14, R.89, G.128, S.129, D.130, D.132 Ligands: EDO.7 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.14, D:G.128, D:S.129, D:D.130, D:D.130 MAN-MAN-MAN-MAN-MAN-MAN.2: 9 residues within 4Å: Chain E: G.13, G.14, Y.37, R.89, G.128, S.129, D.130, D.132 Ligands: EDO.13 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:G.14, E:G.128, E:S.129, E:D.130, E:D.130 MAN-MAN-MAN-MAN-MAN-MAN.3: 9 residues within 4Å: Chain G: G.13, G.14, Y.37, R.89, G.128, S.129, D.130, D.132 Ligands: EDO.18 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:G.14, G:G.128, G:S.129, G:D.130, G:D.130

1 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.4: 7 residues within 4Å: Chain B: G.13, G.14, R.89, G.128, S.129, D.130, D.132 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.14, B:G.128, B:S.129, B:D.130, B:D.130

15 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 7 residues within 4Å: Chain C: K.30, E.64, I.66 Chain F: E.8, V.9, G.10, Y.82 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain F Hydrogen bonds: C:K.30, C:K.30, F:G.10, F:G.10 EDO.6: 6 residues within 4Å: Chain C: E.8, V.9, G.10, Y.82 Chain D: K.30, E.64 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:K.30, D:K.30, C:G.10, C:G.10 EDO.7: 5 residues within 4Å: Chain D: Y.37, K.60, S.129, D.130 Ligands: MAN-MAN-MAN-MAN-MAN-MAN.1 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.60, D:S.129 EDO.8: 7 residues within 4Å: Chain D: E.8, P.16, F.17, T.18, K.124, G.125, R.133 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.18, D:R.133, D:R.133 EDO.9: 2 residues within 4Å: Chain D: M.104, F.108 No protein-ligand interaction detected (PLIP) EDO.10: 2 residues within 4Å: Chain D: G.77, T.96 No protein-ligand interaction detected (PLIP) EDO.11: 2 residues within 4Å: Chain D: Q.21, E.22 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.22 EDO.12: 7 residues within 4Å: Chain D: V.9, G.10, Y.82, K.84, G.85 Chain E: K.30, E.64 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:G.10, D:G.10, D:G.85, E:K.30, E:K.30 EDO.13: 4 residues within 4Å: Chain E: R.89, S.129, D.130 Ligands: MAN-MAN-MAN-MAN-MAN-MAN.2 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.89 EDO.14: 6 residues within 4Å: Chain A: K.30, E.64 Chain E: E.8, V.9, G.10, Y.82 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:K.30, E:G.10 EDO.15: 4 residues within 4Å: Chain F: G.77, S.78, V.79, T.96 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:G.77 EDO.16: 6 residues within 4Å: Chain F: K.30, E.64 Chain G: V.9, G.10, Y.82 Ligands: EDO.19 4 PLIP interactions: 2 interactions with chain G, 2 interactions with chain F Hydrogen bonds: G:G.10, G:G.10, F:K.30, F:K.30 EDO.17: 5 residues within 4Å: Chain B: V.9, G.10, Y.82 Chain G: K.30, E.64 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain B Hydrogen bonds: G:K.30, G:E.64, B:G.10 EDO.18: 6 residues within 4Å: Chain G: Y.37, K.60, R.89, S.129, D.130 Ligands: MAN-MAN-MAN-MAN-MAN-MAN.3 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:K.60, G:K.60, G:R.89, G:R.89, G:S.129 EDO.19: 4 residues within 4Å: Chain F: S.28, E.44 Chain G: T.7 Ligands: EDO.16 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:S.28, F:S.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sivaji, N. et al., Mevo lectin specificity toward high-mannose structures with terminal alpha Man(1,2) alpha Man residues and its implication to inhibition of the entry of Mycobacterium tuberculosis into macrophages. Glycobiology (2021)

Release Date

2021-04-21

Peptides

lectin: ABCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
A

D
B

E
C

F
G

G
F

lectin

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