SMTL ID : 8txt.1

Crystal structure of 05.GC.w13.02 Fab in complex with H5 HA from A/Viet Nam/1203/2004(H5N1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.19 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

2 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.1: 4 residues within 4Å: Chain A: N.27 Chain I: T.101, W.102 Chain J: S.56 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 2 residues within 4Å: Chain E: N.27 Chain K: W.102 No protein-ligand interaction detected (PLIP)

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 5 residues within 4Å: Chain B: E.147, E.150, N.154, T.156 Chain L: S.28 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain C: Q.19, N.27 Chain G: T.101, W.102 Chain H: S.56 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain D: E.147, E.150, N.154, T.156 Chain J: Q.27, S.28 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.147 NAG-NAG.6: 4 residues within 4Å: Chain L: D.1, I.2, Q.3, N.26 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:D.1, L:D.1

7 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.7: 3 residues within 4Å: Chain A: N.169, N.240, A.242 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.169 NAG.8: 5 residues within 4Å: Chain A: K.40, H.41, N.42, A.288, N.290 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.42 Hydrogen bonds: A:N.290 NAG.9: 4 residues within 4Å: Chain C: K.40, H.41, N.42, N.290 No protein-ligand interaction detected (PLIP) NAG.10: 6 residues within 4Å: Chain E: K.40, H.41, N.42, A.288, I.289, N.290 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:N.42 Hydrogen bonds: E:N.290 NAG.11: 4 residues within 4Å: Chain F: E.150, N.154, T.156 Chain H: S.28 3 PLIP interactions: 1 interactions with chain H, 2 interactions with chain F Hydrogen bonds: H:S.28, F:N.154, F:T.156 NAG.12: 3 residues within 4Å: Chain H: D.1, Q.3, N.26 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:D.1 NAG.13: 2 residues within 4Å: Chain J: D.1, N.26 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:D.1, J:D.1, J:N.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McIntire, K.M. et al., Maturation of germinal center B cells after influenza virus vaccination in humans. J.Exp.Med. (2024)

Release Date

2024-06-26

Peptides

Hemagglutinin: ACE
Hemagglutinin: BDF
GC_W13B_B, Fab heavy chain: GIK
GC_w13_B, Fab light chain: HJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

G
H

I
G

K
J

H
L

J
I

L
K

Hemagglutinin

Hemagglutinin

GC_W13B_B, Fab heavy chain

GC_w13_B, Fab light chain

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