SMTL ID : 8txm.1

Crystal structure of 05.GC.w13.02 Fab in complex with H1 HA from A/California/04/2009(H1N1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.25 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

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

NAG-NAG.1: 5 residues within 4Å: Chain A: E.38, K.40, H.41, N.42, N.291 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain E: E.38, K.40, H.41, N.42, N.291 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain I: E.38, K.40, H.41, N.42, N.291 No protein-ligand interaction detected (PLIP)

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

NAG.2: 5 residues within 4Å: Chain A: D.21, K.26, N.27 Chain G: W.103 Chain H: S.57 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain H Hydrophobic interactions: A:K.26 Hydrogen bonds: A:N.27, H:S.57 NAG.5: 4 residues within 4Å: Chain D: D.1, D.2, Q.4, N.27 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.1, D:D.2, D:Q.4 NAG.7: 5 residues within 4Å: Chain E: D.21, K.26, N.27 Chain K: W.103 Chain L: S.57 3 PLIP interactions: 1 interactions with chain L, 2 interactions with chain E Hydrogen bonds: L:S.57, E:N.27 Hydrophobic interactions: E:K.26 NAG.10: 4 residues within 4Å: Chain H: D.1, D.2, Q.4, N.27 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:D.1, H:D.2, H:Q.4 NAG.12: 5 residues within 4Å: Chain C: W.103 Chain D: S.57 Chain I: D.21, K.26, N.27 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain D Hydrophobic interactions: I:K.26 Hydrogen bonds: I:N.27, D:S.57 NAG.15: 4 residues within 4Å: Chain L: D.1, D.2, Q.4, N.27 3 PLIP interactions: 3 interactions with chain L Hydrogen bonds: L:D.1, L:D.2, L:Q.4

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 1 residues within 4Å: Chain A: H.277 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.277 MG.4: 2 residues within 4Å: Chain A: H.12, H.32 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.12, A:H.32 MG.8: 1 residues within 4Å: Chain E: H.277 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:H.277 MG.9: 2 residues within 4Å: Chain E: H.12, H.32 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:H.12, E:H.32 MG.13: 1 residues within 4Å: Chain I: H.277 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:H.277 MG.14: 2 residues within 4Å: Chain I: H.12, H.32 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:H.12, I:H.32

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: AEI
Hemagglutinin: BFJ
GC_w13_B, Fab heavy chain: CGK
GC_w13_B, Fab light chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
A

I
A

B
B

F
B

J
B

C
H

G
H

K
H

D
L

H
L

L
L

Hemagglutinin

Hemagglutinin

GC_w13_B, Fab heavy chain

GC_w13_B, Fab light chain