SMTL ID : 3gbn.1

Crystal Structure of Fab CR6261 in Complex with the 1918 H1N1 influenza virus hemagglutinin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

3 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-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.1: 1 residues within 4Å: Chain A: N.15 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.14: 1 residues within 4Å: Chain E: N.15 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.27: 1 residues within 4Å: Chain I: N.15 No protein-ligand interaction detected (PLIP)

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

NAG.2: 6 residues within 4Å: Chain A: N.68, E.70, E.90, N.91, C.94, R.225 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.70 Hydrogen bonds: A:N.68, A:R.225 Water bridges: A:N.91, A:N.91 NAG.6: 4 residues within 4Å: Chain B: A.147, E.150, N.154, T.156 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.147 NAG.15: 6 residues within 4Å: Chain E: N.68, E.70, E.90, N.91, C.94, R.225 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:E.70 Hydrogen bonds: E:N.68, E:R.225 Water bridges: E:N.91, E:N.91 NAG.19: 4 residues within 4Å: Chain F: A.147, E.150, N.154, T.156 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:A.147, F:T.156 NAG.28: 6 residues within 4Å: Chain I: N.68, E.70, E.90, N.91, C.94, R.225 5 PLIP interactions: 5 interactions with chain I Hydrophobic interactions: I:E.70 Hydrogen bonds: I:N.68, I:R.225 Water bridges: I:N.91, I:N.91 NAG.32: 4 residues within 4Å: Chain J: A.147, E.150, N.154, T.156 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:A.147

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

EDO.3: 5 residues within 4Å: Chain A: V.20, D.21, K.315, R.317 Chain B: N.104 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.21, A:D.21, A:K.315, A:R.317, B:N.104 EDO.9: 8 residues within 4Å: Chain B: Y.24, D.37, L.118, K.121, R.153, N.154, G.155 Ligands: GOL.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.40, B:N.154 Water bridges: B:Q.125 EDO.10: 4 residues within 4Å: Chain B: G.1 Chain F: N.114, N.117 Ligands: GOL.4 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:N.117, B:G.1 Water bridges: F:N.114 EDO.11: 7 residues within 4Å: Chain A: D.5 Chain B: N.28, E.29, Q.30, K.143, C.144, D.145 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:D.5, B:E.29, B:Q.30, B:Q.30, B:C.144 EDO.13: 5 residues within 4Å: Chain C: G.27, F.29, R.30, S.31, Y.32 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.31, C:S.31 Water bridges: C:S.25 EDO.16: 5 residues within 4Å: Chain E: V.20, D.21, K.315, R.317 Chain F: N.104 5 PLIP interactions: 1 interactions with chain F, 4 interactions with chain E Hydrogen bonds: F:N.104, E:D.21, E:D.21, E:K.315, E:R.317 EDO.22: 8 residues within 4Å: Chain F: Y.24, D.37, L.118, K.121, R.153, N.154, G.155 Ligands: GOL.20 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:S.40, F:N.154 Water bridges: F:Q.125 EDO.23: 4 residues within 4Å: Chain F: G.1 Chain J: N.114, N.117 Ligands: GOL.17 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain J Hydrogen bonds: F:G.1, J:N.117 Water bridges: J:N.114 EDO.24: 7 residues within 4Å: Chain E: D.5 Chain F: N.28, E.29, Q.30, K.143, C.144, D.145 5 PLIP interactions: 1 interactions with chain E, 4 interactions with chain F Hydrogen bonds: E:D.5, F:E.29, F:Q.30, F:Q.30, F:C.144 EDO.26: 5 residues within 4Å: Chain G: G.27, F.29, R.30, S.31, Y.32 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:S.31, G:S.31 Water bridges: G:S.25 EDO.29: 5 residues within 4Å: Chain I: V.20, D.21, K.315, R.317 Chain J: N.104 5 PLIP interactions: 1 interactions with chain J, 4 interactions with chain I Hydrogen bonds: J:N.104, I:D.21, I:D.21, I:K.315, I:R.317 EDO.35: 8 residues within 4Å: Chain J: Y.24, D.37, L.118, K.121, R.153, N.154, G.155 Ligands: GOL.33 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:S.40, J:N.154 Water bridges: J:Q.125 EDO.36: 4 residues within 4Å: Chain B: N.114, N.117 Chain J: G.1 Ligands: GOL.30 3 PLIP interactions: 1 interactions with chain J, 2 interactions with chain B Hydrogen bonds: J:G.1, B:N.117 Water bridges: B:N.114 EDO.37: 7 residues within 4Å: Chain I: D.5 Chain J: N.28, E.29, Q.30, K.143, C.144, D.145 5 PLIP interactions: 4 interactions with chain J, 1 interactions with chain I Hydrogen bonds: J:E.29, J:Q.30, J:Q.30, J:C.144, I:D.5 EDO.39: 5 residues within 4Å: Chain K: G.27, F.29, R.30, S.31, Y.32 3 PLIP interactions: 3 interactions with chain K Hydrogen bonds: K:S.31, K:S.31 Water bridges: K:S.25

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: R.323 Chain B: G.1, I.6, A.7, L.108 Ligands: EDO.10 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Water bridges: A:R.323, B:D.112 Hydrogen bonds: B:G.1, B:G.1, B:L.108 GOL.7: 7 residues within 4Å: Chain B: A.36, D.37, Q.38, K.39, E.150, R.153 Ligands: EDO.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.38, B:K.39, B:E.150 GOL.17: 6 residues within 4Å: Chain E: R.323 Chain F: G.1, I.6, A.7, L.108 Ligands: EDO.23 5 PLIP interactions: 1 interactions with chain E, 4 interactions with chain F Water bridges: E:R.323, F:D.112 Hydrogen bonds: F:G.1, F:G.1, F:L.108 GOL.20: 7 residues within 4Å: Chain F: A.36, D.37, Q.38, K.39, E.150, R.153 Ligands: EDO.22 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:Q.38, F:K.39, F:E.150 GOL.30: 6 residues within 4Å: Chain I: R.323 Chain J: G.1, I.6, A.7, L.108 Ligands: EDO.36 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain I Hydrogen bonds: J:G.1, J:G.1, J:L.108 Water bridges: I:R.323 GOL.33: 7 residues within 4Å: Chain J: A.36, D.37, Q.38, K.39, E.150, R.153 Ligands: EDO.35 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:Q.38, J:K.39, J:E.150

3 x ETX: 2-ETHOXYETHANOL(Non-covalent)

ETX.5: 9 residues within 4Å: Chain A: V.23, L.24 Chain B: L.102, E.105 Chain F: K.51, E.103, R.106, T.107, F.110 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain F Hydrophobic interactions: A:L.24, F:R.106, F:F.110 Hydrogen bonds: F:K.51 Water bridges: F:R.106, F:R.106 ETX.18: 9 residues within 4Å: Chain E: V.23, L.24 Chain F: L.102, E.105 Chain J: K.51, E.103, R.106, T.107, F.110 6 PLIP interactions: 5 interactions with chain J, 1 interactions with chain E Hydrophobic interactions: J:R.106, J:F.110, E:L.24 Hydrogen bonds: J:K.51 Water bridges: J:R.106, J:R.106 ETX.31: 9 residues within 4Å: Chain B: K.51, E.103, R.106, T.107, F.110 Chain I: V.23, L.24 Chain J: L.102, E.105 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain I Hydrophobic interactions: B:R.106, B:F.110, I:L.24 Hydrogen bonds: B:K.51 Water bridges: B:R.106, B:R.106

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 6 residues within 4Å: Chain B: Y.24, H.25, H.26, G.33, A.35, R.153 Ligand excluded by PLIP CL.21: 6 residues within 4Å: Chain F: Y.24, H.25, H.26, G.33, A.35, R.153 Ligand excluded by PLIP CL.34: 6 residues within 4Å: Chain J: Y.24, H.25, H.26, G.33, A.35, R.153 Ligand excluded by PLIP

3 x UNL: UNKNOWN LIGAND

UNL.12: 8 residues within 4Å: Chain B: E.120, S.124 Chain J: F.9, R.116, Y.119, E.120, K.123, E.132 11 PLIP interactions: 8 interactions with chain J, 3 interactions with chain B Hydrogen bonds: J:R.116, J:R.116, J:Y.119, J:K.123, B:S.124, B:S.124 Water bridges: J:G.134, J:G.134, J:N.135, J:G.136, B:S.124 UNL.25: 8 residues within 4Å: Chain B: F.9, R.116, Y.119, E.120, K.123, E.132 Chain F: E.120, S.124 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain F Hydrogen bonds: B:R.116, B:R.116, B:K.123, F:S.124, F:S.124 Water bridges: B:G.134, B:G.134, B:N.135, B:G.136, F:S.124 UNL.38: 8 residues within 4Å: Chain F: F.9, R.116, Y.119, E.120, K.123, E.132 Chain J: E.120, S.124 11 PLIP interactions: 8 interactions with chain F, 3 interactions with chain J Hydrogen bonds: F:R.116, F:R.116, F:E.120, F:K.123, J:S.124, J:S.124 Water bridges: F:G.134, F:G.134, F:N.135, F:G.136, J:S.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ekiert, D.C. et al., Antibody recognition of a highly conserved influenza virus epitope. Science (2009)

Release Date

2009-03-10

Peptides

Hemagglutinin: AEI
Hemagglutinin: BFJ
Fab Heavy Chain: CGK
Fab Lambda 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

Fab Heavy Chain

Fab Lambda Light Chain

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