SMTL ID : 5d9q.1

Crystal Structure of the BG505 SOSIP gp140 HIV-1 Env trimer in Complex with the Broadly Neutralizing Fab PGT122 and scFv NIH45-46

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 4.40 Å

Oligo State

hetero-3-3-3-3-3-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: 4 residues within 4Å: Chain A: E.57, N.58 Chain B: L.9, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.3: 4 residues within 4Å: Chain A: T.105, N.118, S.120, Y.135 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.7: 10 residues within 4Å: Chain A: E.181, P.182, N.232, N.346, G.348, R.412, C.413, V.414, S.415 Ligands: NAG-NAG.13 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.15: 3 residues within 4Å: Chain F: E.57, N.58 Chain G: S.17 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.17: 4 residues within 4Å: Chain F: T.105, N.118, S.120, Y.135 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.21: 8 residues within 4Å: Chain F: E.181, P.182, N.232, N.346, R.412, V.414, S.415 Ligands: NAG-NAG.27 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.29: 4 residues within 4Å: Chain K: E.57, N.58 Chain L: G.16, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.31: 4 residues within 4Å: Chain K: T.105, N.118, S.120, Y.135 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.35: 10 residues within 4Å: Chain K: E.181, P.182, N.232, N.346, G.348, R.412, C.413, V.414, S.415 Ligands: NAG-NAG.41 No protein-ligand interaction detected (PLIP)

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.2: 12 residues within 4Å: Chain A: N.107, T.109 Chain C: W.86, D.87, T.92 Chain D: Y.33, D.56, N.58, R.102, W.113, F.114, T.115 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.56, D:Y.33, D:Y.33, D:R.102, D:T.115 NAG-NAG-BMA-MAN.16: 12 residues within 4Å: Chain F: N.107, T.109 Chain H: W.86, D.87, T.92 Chain I: Y.33, D.56, N.58, R.102, W.113, F.114, T.115 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:D.56, I:Y.33, I:R.102, I:T.115 NAG-NAG-BMA-MAN.30: 12 residues within 4Å: Chain K: N.107, T.109 Chain M: W.86, D.87, T.92 Chain N: Y.33, D.56, N.58, R.102, W.113, F.114, T.115 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:Y.33, N:Y.33, N:R.102, N:T.115

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

NAG-NAG.4: 5 residues within 4Å: Chain A: T.98, Q.100, S.120, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 7 residues within 4Å: Chain A: Q.263, N.265, N.301, V.302, S.303, V.414 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.10 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain A: N.355, S.357 Ligands: NAG-NAG.12, NAG.46 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain A: N.361 Ligands: NAG-NAG.11, NAG.46 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain A: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.7 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain A: N.429, N.430 Chain E: R.44, Q.234 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.44, E:Q.234 NAG-NAG.18: 5 residues within 4Å: Chain F: T.98, Q.100, S.120, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 8 residues within 4Å: Chain F: Q.263, N.265, N.301, V.302, S.303, S.381, V.414 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.24 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 4 residues within 4Å: Chain F: N.355, S.357 Ligands: NAG-NAG.26, NAG.52 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain F: N.361 Ligands: NAG-NAG.25, NAG.52 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 3 residues within 4Å: Chain F: P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.21 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 4 residues within 4Å: Chain F: N.429, N.430 Chain J: R.44, Q.234 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:R.44, J:Q.234 NAG-NAG.32: 4 residues within 4Å: Chain K: T.98, Q.100, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 7 residues within 4Å: Chain K: Q.263, N.265, N.301, V.302, S.303, V.414 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.38 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 3 residues within 4Å: Chain K: N.355 Ligands: NAG-NAG.40, NAG.58 No protein-ligand interaction detected (PLIP) NAG-NAG.40: 3 residues within 4Å: Chain K: N.361 Ligands: NAG-NAG.39, NAG.58 No protein-ligand interaction detected (PLIP) NAG-NAG.41: 3 residues within 4Å: Chain K: P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.35 No protein-ligand interaction detected (PLIP) NAG-NAG.42: 4 residues within 4Å: Chain K: N.429, N.430 Chain O: R.44, Q.234 2 PLIP interactions: 2 interactions with chain O Hydrogen bonds: O:R.44, O:Q.234

6 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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.5: 6 residues within 4Å: Chain A: R.162, I.164, N.167 Chain E: R.19, R.84 Chain K: R.278 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.19, E:R.19, E:R.19 NAG-NAG-BMA-MAN-MAN-MAN-MAN.9: 6 residues within 4Å: Chain A: N.271, N.272, T.273, I.292 Chain C: G.63, T.64 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.292 NAG-NAG-BMA-MAN-MAN-MAN-MAN.19: 6 residues within 4Å: Chain A: R.278 Chain F: R.162, I.164, N.167 Chain J: R.19, R.84 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:R.19, J:R.19, J:R.19 NAG-NAG-BMA-MAN-MAN-MAN-MAN.23: 6 residues within 4Å: Chain F: N.271, N.272, T.273, I.292 Chain H: G.63, T.64 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:I.292 NAG-NAG-BMA-MAN-MAN-MAN-MAN.33: 6 residues within 4Å: Chain F: R.278 Chain K: R.162, I.164, N.167 Chain O: R.19, R.84 2 PLIP interactions: 2 interactions with chain O Hydrogen bonds: O:R.19, O:R.19, O:R.19 NAG-NAG-BMA-MAN-MAN-MAN-MAN.37: 6 residues within 4Å: Chain K: N.271, N.272, T.273, I.292 Chain M: G.63, T.64 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:I.292

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]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-MAN-MAN-MAN-MAN-MAN-MAN.6: 10 residues within 4Å: Chain A: N.204, T.206, G.207, P.208, H.321 Chain E: S.168, R.204, W.205, G.206, A.207 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.204 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.20: 10 residues within 4Å: Chain F: N.204, T.206, G.207, P.208, H.321 Chain J: S.168, R.204, W.205, G.206, A.207 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:R.204 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.34: 10 residues within 4Å: Chain K: N.204, T.206, G.207, P.208, H.321 Chain O: S.168, R.204, W.205, G.206, A.207 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:R.204

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-MAN-MAN-MAN-MAN.10: 20 residues within 4Å: Chain A: N.265, T.267, R.296, H.299, N.301, D.380, S.381, T.383 Chain C: S.22, N.42, N.43, P.58, G.59, S.60 Chain D: R.103, I.104, Y.105, G.106, V.107 Ligands: NAG-NAG.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.296, A:R.296 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.24: 19 residues within 4Å: Chain F: N.265, T.267, R.296, H.299, N.301, D.380, S.381, T.383 Chain H: S.22, N.42, N.43, G.59, S.60 Chain I: R.103, I.104, Y.105, G.106, V.107 Ligands: NAG-NAG.22 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.296, F:R.296 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.38: 20 residues within 4Å: Chain K: N.265, T.267, R.296, H.299, N.301, D.380, S.381, T.383 Chain M: S.22, N.42, N.43, P.58, G.59, S.60 Chain N: R.103, I.104, Y.105, G.106, V.107 Ligands: NAG-NAG.36 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:R.296, K:R.296

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

NAG.43: 2 residues within 4Å: Chain A: N.103, D.110 Ligand excluded by PLIP NAG.44: 5 residues within 4Å: Chain A: E.245, N.246, T.248 Chain E: G.169, Y.229 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain A: N.308, W.364 Ligand excluded by PLIP NAG.46: 5 residues within 4Å: Chain A: N.332, S.333, S.357 Ligands: NAG-NAG.11, NAG-NAG.12 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain B: N.100, S.102 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain B: E.123, N.126 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain F: N.103, D.110 Ligand excluded by PLIP NAG.50: 6 residues within 4Å: Chain F: E.245, N.246, T.248 Chain J: S.168, G.169, Y.229 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain F: N.308, W.364 Ligand excluded by PLIP NAG.52: 5 residues within 4Å: Chain F: N.332, S.333, S.357 Ligands: NAG-NAG.25, NAG-NAG.26 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain G: N.100, S.102 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain G: E.123, N.126 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain K: N.103, D.110 Ligand excluded by PLIP NAG.56: 5 residues within 4Å: Chain K: E.245, N.246, T.248 Chain O: G.169, Y.229 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain K: N.308, W.364 Ligand excluded by PLIP NAG.58: 5 residues within 4Å: Chain K: N.332, S.333, S.357 Ligands: NAG-NAG.39, NAG-NAG.40 Ligand excluded by PLIP NAG.59: 2 residues within 4Å: Chain L: N.100, S.102 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain L: E.123, N.126 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jardine, J.G. et al., Minimally Mutated HIV-1 Broadly Neutralizing Antibodies to Guide Reductionist Vaccine Design. Plos Pathog. (2016)

Release Date

2016-08-17

Peptides

Envelope glycoprotein gp120: AFK
Envelope glycoprotein gp41: BGL
PGT122 light chain,Ig lambda-3 chain C regions: CHM
PGT122 heavy chain,IgG H chain: DIN
NIH45-46 single chain Fv: EJO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

F
A

K
J

B
B

G
C

L
K

C
L

H
E

M
M

D
H

I
F

N
N

E
D

J
I

O
O

Envelope glycoprotein gp120

Envelope glycoprotein gp41

PGT122 light chain,Ig lambda-3 chain C regions

PGT122 heavy chain,IgG H chain

NIH45-46 single chain Fv

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