SMTL ID : 6oz4.1

Crystal structure of broadly neutralizing antibody N49P6 Fab in complex with HIV-1 BG505 SOSIP.664 Env trimer ectodomain.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.05 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

9 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: T.105, N.118, Y.135, D.290 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.135 NAG-NAG-BMA.5: 9 residues within 4Å: Chain A: E.181, P.182, L.231, N.232, C.347, G.348, V.414, S.415 Ligands: NAG-NAG.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.348 NAG-NAG-BMA.9: 5 residues within 4Å: Chain A: N.332, T.341, S.357 Ligands: NAG-NAG.10, NAG-NAG.10 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 4 residues within 4Å: Chain E: T.105, N.118, Y.135, D.290 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.135 NAG-NAG-BMA.24: 9 residues within 4Å: Chain E: E.181, P.182, L.231, N.232, C.347, G.348, V.414, S.415 Ligands: NAG-NAG.31 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:G.348 NAG-NAG-BMA.28: 5 residues within 4Å: Chain E: N.332, T.341, S.357 Ligands: NAG-NAG.29, NAG-NAG.29 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.39: 4 residues within 4Å: Chain I: T.105, N.118, Y.135, D.290 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:Y.135 NAG-NAG-BMA.43: 9 residues within 4Å: Chain I: E.181, P.182, L.231, N.232, C.347, G.348, V.414, S.415 Ligands: NAG-NAG.50 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:G.348 NAG-NAG-BMA.47: 5 residues within 4Å: Chain I: N.332, T.341, S.357 Ligands: NAG-NAG.48, NAG-NAG.48 No protein-ligand interaction detected (PLIP)

21 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: 6 residues within 4Å: Chain A: T.98, S.120, F.121, N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: N.204, T.206, S.244, H.321 Ligands: NAG.14 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 7 residues within 4Å: Chain A: Q.263, N.265, N.301, V.302, S.303, S.381 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.8 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain A: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 6 residues within 4Å: Chain A: N.355, S.357 Ligands: NAG-NAG-BMA.9, NAG-NAG-BMA.9, NAG-NAG-BMA.9, NAG-NAG.11 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain A: N.361 Ligands: NAG-NAG.10 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain A: N.232, P.261, N.416 Ligands: NAG-NAG-BMA.5 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 6 residues within 4Å: Chain E: T.98, S.120, F.121, N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 5 residues within 4Å: Chain E: N.204, T.206, S.244, H.321 Ligands: NAG.33 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 7 residues within 4Å: Chain E: Q.263, N.265, N.301, V.302, S.303, S.381 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.27 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 2 residues within 4Å: Chain E: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 6 residues within 4Å: Chain E: N.355, S.357 Ligands: NAG-NAG-BMA.28, NAG-NAG-BMA.28, NAG-NAG-BMA.28, NAG-NAG.30 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 2 residues within 4Å: Chain E: N.361 Ligands: NAG-NAG.29 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 4 residues within 4Å: Chain E: N.232, P.261, N.416 Ligands: NAG-NAG-BMA.24 No protein-ligand interaction detected (PLIP) NAG-NAG.40: 6 residues within 4Å: Chain I: T.98, S.120, F.121, N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.42: 5 residues within 4Å: Chain I: N.204, T.206, S.244, H.321 Ligands: NAG.52 No protein-ligand interaction detected (PLIP) NAG-NAG.44: 7 residues within 4Å: Chain I: Q.263, N.265, N.301, V.302, S.303, S.381 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.46 No protein-ligand interaction detected (PLIP) NAG-NAG.45: 2 residues within 4Å: Chain I: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.48: 6 residues within 4Å: Chain I: N.355, S.357 Ligands: NAG-NAG-BMA.47, NAG-NAG-BMA.47, NAG-NAG-BMA.47, NAG-NAG.49 No protein-ligand interaction detected (PLIP) NAG-NAG.49: 2 residues within 4Å: Chain I: N.361 Ligands: NAG-NAG.48 No protein-ligand interaction detected (PLIP) NAG-NAG.50: 4 residues within 4Å: Chain I: N.232, P.261, N.416 Ligands: NAG-NAG-BMA.43 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN: 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.3: 5 residues within 4Å: Chain A: R.162, N.167, T.168 Chain C: R.18 Chain I: R.278 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.22: 5 residues within 4Å: Chain A: R.278 Chain E: R.162, N.167, T.168 Chain G: R.18 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.41: 5 residues within 4Å: Chain E: R.278 Chain I: R.162, N.167, T.168 Chain K: R.18 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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-MAN-MAN-MAN.8: 5 residues within 4Å: Chain A: T.267, H.299, N.301, T.383 Ligands: NAG-NAG.6 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.27: 5 residues within 4Å: Chain E: T.267, H.299, N.301, T.383 Ligands: NAG-NAG.25 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.46: 5 residues within 4Å: Chain I: T.267, H.299, N.301, T.383 Ligands: NAG-NAG.44 No protein-ligand interaction detected (PLIP)

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

NAG.13: 3 residues within 4Å: Chain A: N.103, R.113, K.117 Ligand excluded by PLIP NAG.14: 7 residues within 4Å: Chain A: N.246, T.248 Chain C: V.111 Chain D: N.27, Y.28, F.87 Ligands: NAG-NAG.4 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.324 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.308 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: N.100, S.102 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: N.107, E.110 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: E.123, N.126 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain E: N.103, R.113, K.117 Ligand excluded by PLIP NAG.33: 7 residues within 4Å: Chain E: N.246, T.248 Chain G: V.111 Chain H: N.27, Y.28, F.87 Ligands: NAG-NAG.23 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain E: N.324 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain E: N.308 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain F: N.100, S.102 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain F: N.107, E.110 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain F: E.123, N.126 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain I: N.103, R.113, K.117 Ligand excluded by PLIP NAG.52: 7 residues within 4Å: Chain I: N.246, T.248 Chain K: V.111 Chain L: N.27, Y.28, F.87 Ligands: NAG-NAG.42 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain I: N.324 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain I: N.308 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain J: N.100, S.102 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain J: N.107, E.110 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain J: E.123, N.126 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tolbert, W.D. et al., Near-Pan-neutralizing, Plasma Deconvoluted Antibody N49P6 Mimics Host Receptor CD4 in Its Quaternary Interactions with the HIV-1 Envelope Trimer. Mbio (2021)

Release Date

2020-08-19

Peptides

Envelope glycoprotein gp160: AEI
Envelope glycoprotein gp41: BFJ
N49P6 antibody Fab heavy chain: CGK
N49P6 antibody light chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

E
G

I
G

B
B

F
B

J
B

C
H

G
H

K
H

D
L

H
L

L
L

Envelope glycoprotein gp160

Envelope glycoprotein gp41

N49P6 antibody Fab heavy chain

N49P6 antibody light chain

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