SMTL ID : 7kc1.1

Cryo-EM structure of SRR2899884.46167H+MEDI8852L fab in complex with Victoria HA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

9 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 9 residues within 4Å: Chain A: T.40, N.54, A.55 Chain C: G.26, D.27, Y.33, T.105, F.107, G.108 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.2: 7 residues within 4Å: Chain A: N.181, I.258, L.260 Chain E: Y.235, R.238, N.241 Ligands: NAG-NAG-BMA-MAN-MAN.3 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.258 NAG-NAG-BMA-MAN-MAN.3: 8 residues within 4Å: Chain A: A.179, R.217, N.262, S.263, T.264 Chain E: I.233, Y.235 Ligands: NAG-NAG-BMA-MAN-MAN.2 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.5: 9 residues within 4Å: Chain E: T.40, N.54, A.55 Chain G: G.26, D.27, Y.33, T.105, F.107, G.108 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.6: 7 residues within 4Å: Chain E: N.181, I.258, L.260 Chain I: Y.235, R.238, N.241 Ligands: NAG-NAG-BMA-MAN-MAN.7 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:I.258 NAG-NAG-BMA-MAN-MAN.7: 8 residues within 4Å: Chain E: A.179, R.217, N.262, S.263, T.264 Chain I: I.233, Y.235 Ligands: NAG-NAG-BMA-MAN-MAN.6 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.9: 9 residues within 4Å: Chain I: T.40, N.54, A.55 Chain K: G.26, D.27, Y.33, T.105, F.107, G.108 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.10: 7 residues within 4Å: Chain A: Y.235, R.238, N.241 Chain I: N.181, I.258, L.260 Ligands: NAG-NAG-BMA-MAN-MAN.11 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:I.258 NAG-NAG-BMA-MAN-MAN.11: 8 residues within 4Å: Chain A: I.233, Y.235 Chain I: A.179, R.217, N.262, S.263, T.264 Ligands: NAG-NAG-BMA-MAN-MAN.10 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.4: 3 residues within 4Å: Chain A: N.301, V.313, N.314 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 3 residues within 4Å: Chain E: N.301, V.313, N.314 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 3 residues within 4Å: Chain I: N.301, V.313, N.314 No protein-ligand interaction detected (PLIP)

15 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.13: 1 residues within 4Å: Chain A: N.38 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: E.78, N.79, K.108, Y.110 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.142, T.144 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.149 Ligand excluded by PLIP NAG.17: 5 residues within 4Å: Chain B: A.147, G.150, S.151, N.154, T.156 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain E: N.38 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain E: E.78, N.79, K.108, Y.110 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain E: N.142, T.144 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain E: N.149 Ligand excluded by PLIP NAG.22: 5 residues within 4Å: Chain F: A.147, G.150, S.151, N.154, T.156 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain I: N.38 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain I: E.78, N.79, K.108, Y.110 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain I: N.142, T.144 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain I: N.149 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain J: A.147, G.150, S.151, N.154, T.156 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chuang, G.Y. et al., Sequence-Signature Optimization Enables Improved Identification of Human HV6-1-Derived Class Antibodies That Neutralize Diverse Influenza A Viruses. Front Immunol (2021)

Release Date

2021-05-12

Peptides

Hemagglutinin: AEI
Fusion protein of Hemagglutinin and Envelope glycoprotein: BFJ
Fab heavy chain: CGK
Fab light chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
C

I
G

B
B

F
D

J
I

C
H

G
E

K
J

D
L

H
F

L
K

Hemagglutinin

Fusion protein of Hemagglutinin and Envelope glycoprotein

Fab heavy chain

Fab light chain

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