SMTL ID : 1mql.2 (1 other biounit)

BHA of Ukr/63

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-6-6-mer

Ligands

14 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Non-functional Binders)

NAG.1: 3 residues within 4Å: Chain A: N.38, T.318 Chain B: L.52 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.38, A:N.38, A:T.318 NAG.3: 1 residues within 4Å: Ligands: NDG.2 No protein-ligand interaction detected (PLIP) NAG.4: 4 residues within 4Å: Chain A: N.165, T.167 Chain E: S.219 Ligands: NDG.18 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.219, E:S.219 NAG.6: 5 residues within 4Å: Chain A: P.221, W.222 Chain C: T.167 Ligands: MAN.7, NDG.13 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:T.167 Hydrogen bonds: A:W.222 NAG.12: 3 residues within 4Å: Chain C: N.81, F.120, I.121 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.81, C:N.81, C:N.81 NAG.23: 5 residues within 4Å: Chain C: S.219, W.222 Chain E: N.165, T.167 Ligands: NDG.14 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain E Hydrogen bonds: C:S.219, C:S.219, C:W.222, E:N.165, E:T.167 NAG.25: 5 residues within 4Å: Chain F: A.147, E.150, S.151, N.154, T.156 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:N.154, F:N.154, F:N.154 NAG.26: 3 residues within 4Å: Chain G: N.38, T.318 Chain H: L.52 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:N.38, G:N.38 NAG.28: 1 residues within 4Å: Ligands: NDG.27 No protein-ligand interaction detected (PLIP) NAG.29: 4 residues within 4Å: Chain G: N.165, T.167 Chain K: S.219 Ligands: NDG.43 3 PLIP interactions: 2 interactions with chain K, 1 interactions with chain G Hydrogen bonds: K:S.219, K:S.219, G:T.167 NAG.31: 5 residues within 4Å: Chain G: P.221, W.222 Chain I: T.167 Ligands: MAN.32, NDG.38 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain G Hydrophobic interactions: I:T.167 Hydrogen bonds: G:W.222 NAG.37: 3 residues within 4Å: Chain I: N.81, F.120, I.121 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:N.81, I:N.81, I:N.81 NAG.48: 5 residues within 4Å: Chain I: S.219, W.222 Chain K: N.165, T.167 Ligands: NDG.39 6 PLIP interactions: 3 interactions with chain I, 3 interactions with chain K Hydrogen bonds: I:S.219, I:S.219, I:W.222, K:N.165, K:T.167, K:T.167 NAG.50: 5 residues within 4Å: Chain L: A.147, E.150, S.151, N.154, T.156 3 PLIP interactions: 3 interactions with chain L Hydrogen bonds: L:N.154, L:N.154, L:N.154

24 x NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-covalent)

NDG.2: 6 residues within 4Å: Chain A: Q.80, N.81, E.119, F.120, R.150 Ligands: NAG.3 Ligand excluded by PLIP NDG.5: 5 residues within 4Å: Chain A: N.285, V.297, N.298 Chain B: E.69 Ligands: NDG.9 Ligand excluded by PLIP NDG.9: 2 residues within 4Å: Chain A: K.299 Ligands: NDG.5 Ligand excluded by PLIP NDG.10: 5 residues within 4Å: Chain B: A.147, E.150, S.151, N.154, T.156 Ligand excluded by PLIP NDG.11: 4 residues within 4Å: Chain C: N.38, T.318 Chain D: L.52 Chain I: D.275 Ligand excluded by PLIP NDG.13: 4 residues within 4Å: Chain A: S.219 Chain C: N.165, T.167 Ligands: NAG.6 Ligand excluded by PLIP NDG.14: 4 residues within 4Å: Chain C: P.221, W.222 Ligands: MAN.15, NAG.23 Ligand excluded by PLIP NDG.17: 4 residues within 4Å: Chain D: E.150, S.151, N.154, T.156 Ligand excluded by PLIP NDG.18: 4 residues within 4Å: Chain E: P.221, W.222 Ligands: NAG.4, MAN.19 Ligand excluded by PLIP NDG.21: 4 residues within 4Å: Chain E: T.24, N.38, A.39, K.315 Ligand excluded by PLIP NDG.22: 5 residues within 4Å: Chain E: Q.80, N.81, E.119, F.120, R.150 Ligand excluded by PLIP NDG.24: 4 residues within 4Å: Chain E: N.285, V.297, N.298 Chain F: E.69 Ligand excluded by PLIP NDG.27: 6 residues within 4Å: Chain G: Q.80, N.81, E.119, F.120, R.150 Ligands: NAG.28 Ligand excluded by PLIP NDG.30: 5 residues within 4Å: Chain G: N.285, V.297, N.298 Chain H: E.69 Ligands: NDG.34 Ligand excluded by PLIP NDG.34: 2 residues within 4Å: Chain G: K.299 Ligands: NDG.30 Ligand excluded by PLIP NDG.35: 5 residues within 4Å: Chain H: A.147, E.150, S.151, N.154, T.156 Ligand excluded by PLIP NDG.36: 4 residues within 4Å: Chain C: D.275 Chain I: N.38, T.318 Chain J: L.52 Ligand excluded by PLIP NDG.38: 4 residues within 4Å: Chain G: S.219 Chain I: N.165, T.167 Ligands: NAG.31 Ligand excluded by PLIP NDG.39: 4 residues within 4Å: Chain I: P.221, W.222 Ligands: MAN.40, NAG.48 Ligand excluded by PLIP NDG.42: 4 residues within 4Å: Chain J: E.150, S.151, N.154, T.156 Ligand excluded by PLIP NDG.43: 4 residues within 4Å: Chain K: P.221, W.222 Ligands: NAG.29, MAN.44 Ligand excluded by PLIP NDG.46: 4 residues within 4Å: Chain K: T.24, N.38, A.39, K.315 Ligand excluded by PLIP NDG.47: 5 residues within 4Å: Chain K: Q.80, N.81, E.119, F.120, R.150 Ligand excluded by PLIP NDG.49: 4 residues within 4Å: Chain K: N.285, V.297, N.298 Chain L: E.69 Ligand excluded by PLIP

12 x MAN: alpha-D-mannopyranose(Non-covalent)(Non-functional Binders)

MAN.7: 3 residues within 4Å: Chain A: W.222 Ligands: NAG.6, MAN.8 No protein-ligand interaction detected (PLIP) MAN.8: 1 residues within 4Å: Ligands: MAN.7 No protein-ligand interaction detected (PLIP) MAN.15: 2 residues within 4Å: Ligands: NDG.14, MAN.16 No protein-ligand interaction detected (PLIP) MAN.16: 1 residues within 4Å: Ligands: MAN.15 No protein-ligand interaction detected (PLIP) MAN.19: 3 residues within 4Å: Chain E: W.222 Ligands: NDG.18, MAN.20 No protein-ligand interaction detected (PLIP) MAN.20: 1 residues within 4Å: Ligands: MAN.19 No protein-ligand interaction detected (PLIP) MAN.32: 3 residues within 4Å: Chain G: W.222 Ligands: NAG.31, MAN.33 No protein-ligand interaction detected (PLIP) MAN.33: 1 residues within 4Å: Ligands: MAN.32 No protein-ligand interaction detected (PLIP) MAN.40: 2 residues within 4Å: Ligands: NDG.39, MAN.41 No protein-ligand interaction detected (PLIP) MAN.41: 1 residues within 4Å: Ligands: MAN.40 No protein-ligand interaction detected (PLIP) MAN.44: 3 residues within 4Å: Chain K: W.222 Ligands: NDG.43, MAN.45 No protein-ligand interaction detected (PLIP) MAN.45: 1 residues within 4Å: Ligands: MAN.44 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ha, Y. et al., X-ray structure of the hemagglutinin of a potential H3 avian progenitor of the 1968 Hong Kong pandemic influenza virus. Virology (2003)

Release Date

2003-08-26

Peptides

Hemagglutinin HA1 chain: ACEGIK
Hemagglutinin HA2 chain: BDFHJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
D

E
G

G
A

I
D

K
G

B
B

D
E

F
H

H
B

J
E

L
H

Hemagglutinin HA1 chain

Hemagglutinin HA2 chain

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