SMTL ID : 5js9.1

Uncleaved prefusion optimized gp140 trimer with an engineered 8-residue HR1 turn bound to broadly neutralizing antibodies 8ANC195 and PGT128

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 6.92 Å

Oligo State

hetero-3-3-3-3-3-3-mer

Ligands

12 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: R.112 Chain C: N.117, S.119, Y.134, D.289 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain C: V.143, R.161, N.166 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain C: N.354, S.356, R.386 Ligands: NAG-NAG-BMA.10, NAG-NAG-BMA.10, NAG-NAG-BMA.11 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain C: N.231, L.234, P.260, N.415 Ligands: NAG-NAG-BMA-MAN-MAN.8 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 5 residues within 4Å: Chain G: R.112 Chain I: N.117, S.119, Y.134, D.289 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain I: V.143, R.161, N.166 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 6 residues within 4Å: Chain I: N.354, S.356, R.386 Ligands: NAG-NAG-BMA.28, NAG-NAG-BMA.28, NAG-NAG-BMA.29 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 5 residues within 4Å: Chain I: N.231, L.234, P.260, N.415 Ligands: NAG-NAG-BMA-MAN-MAN.26 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 5 residues within 4Å: Chain M: R.112 Chain O: N.117, S.119, Y.134, D.289 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 3 residues within 4Å: Chain O: V.143, R.161, N.166 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 6 residues within 4Å: Chain O: N.354, S.356, R.386 Ligands: NAG-NAG-BMA.46, NAG-NAG-BMA.46, NAG-NAG-BMA.47 No protein-ligand interaction detected (PLIP) NAG-NAG.40: 5 residues within 4Å: Chain O: N.231, L.234, P.260, N.415 Ligands: NAG-NAG-BMA-MAN-MAN.44 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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.5: 9 residues within 4Å: Chain C: N.245, T.247, N.248 Chain E: Q.1, H.3, V.5, Q.6, Y.25, G.26 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.1, E:Q.1, E:Q.6 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.23: 9 residues within 4Å: Chain I: N.245, T.247, N.248 Chain K: Q.1, H.3, V.5, Q.6, Y.25, G.26 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:Q.1, K:H.3, K:Q.6 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.41: 9 residues within 4Å: Chain O: N.245, T.247, N.248 Chain Q: Q.1, H.3, V.5, Q.6, Y.25, G.26 1 PLIP interactions: 1 interactions with chain Q Hydrogen bonds: Q:Q.1, Q:Q.1, Q:Q.6

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-(1-6)-[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-MAN-MAN-MAN-MAN-MAN.6: 16 residues within 4Å: Chain A: Y.59, W.60, W.64, T.65, Y.66, H.67, K.72 Chain B: V.89, G.90, N.91, W.92, D.93 Chain C: T.266, H.298, N.300, S.380 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.24: 16 residues within 4Å: Chain G: Y.59, W.60, W.64, T.65, Y.66, H.67, K.72 Chain H: V.89, G.90, N.91, W.92, D.93 Chain I: T.266, H.298, N.300, S.380 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.42: 16 residues within 4Å: Chain M: Y.59, W.60, W.64, T.65, Y.66, H.67, K.72 Chain N: V.89, G.90, N.91, W.92, D.93 Chain O: T.266, H.298, N.300, S.380 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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-MAN-MAN-MAN.7: 11 residues within 4Å: Chain A: A.30, H.55, C.56, A.57, S.58, T.81, P.82 Chain C: N.270, T.272, R.273, G.408 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:T.81, C:Q.407 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.25: 11 residues within 4Å: Chain G: A.30, H.55, C.56, A.57, S.58, T.81, P.82 Chain I: N.270, T.272, R.273, G.408 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain I Hydrogen bonds: G:T.81, I:Q.407 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.43: 11 residues within 4Å: Chain M: A.30, H.55, C.56, A.57, S.58, T.81, P.82 Chain O: N.270, T.272, R.273, G.408 3 PLIP interactions: 2 interactions with chain M, 1 interactions with chain O Hydrogen bonds: M:T.81, M:T.81, M:T.81, O:Q.407

3 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.8: 11 residues within 4Å: Chain C: K.35, E.180, P.181, K.221, V.223, N.231, N.345, G.347, V.413, S.414 Ligands: NAG-NAG.4 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.347, C:K.35, C:K.35 NAG-NAG-BMA-MAN-MAN.26: 11 residues within 4Å: Chain I: K.35, E.180, P.181, K.221, V.223, N.231, N.345, G.347, V.413, S.414 Ligands: NAG-NAG.22 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:G.347, I:K.35, I:K.35 NAG-NAG-BMA-MAN-MAN.44: 11 residues within 4Å: Chain O: K.35, E.180, P.181, K.221, V.223, N.231, N.345, G.347, V.413, S.414 Ligands: NAG-NAG.40 2 PLIP interactions: 2 interactions with chain O Hydrogen bonds: O:G.347, O:K.35, O:K.35

3 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-2)-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.9: 5 residues within 4Å: Chain C: Q.262, N.264, N.300, V.301, S.302 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.262 NAG-NAG-BMA-MAN-MAN.27: 5 residues within 4Å: Chain I: Q.262, N.264, N.300, V.301, S.302 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:Q.262 NAG-NAG-BMA-MAN-MAN.45: 5 residues within 4Å: Chain O: Q.262, N.264, N.300, V.301, S.302 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:Q.262

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.10: 5 residues within 4Å: Chain C: N.331, N.354, S.356 Ligands: NAG-NAG.3, NAG-NAG.3 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 2 residues within 4Å: Chain C: N.360 Ligands: NAG-NAG.3 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 3 residues within 4Å: Chain C: K.303, A.304, N.307 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.28: 5 residues within 4Å: Chain I: N.331, N.354, S.356 Ligands: NAG-NAG.21, NAG-NAG.21 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.29: 2 residues within 4Å: Chain I: N.360 Ligands: NAG-NAG.21 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.30: 3 residues within 4Å: Chain I: K.303, A.304, N.307 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.46: 5 residues within 4Å: Chain O: N.331, N.354, S.356 Ligands: NAG-NAG.39, NAG-NAG.39 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.47: 2 residues within 4Å: Chain O: N.360 Ligands: NAG-NAG.39 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.48: 3 residues within 4Å: Chain O: K.303, A.304, N.307 No protein-ligand interaction detected (PLIP)

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.13: 24 residues within 4Å: Chain C: K.201, N.203, I.246, H.320 Chain E: T.19, W.55, S.57, S.58, A.59, F.63, R.64, G.65, V.67, L.68, I.69, S.70, A.71, V.72, D.73, L.74, I.81, S.82, S.83, E.85 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:D.73, E:A.71, E:S.57, E:A.59, E:G.65 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.31: 24 residues within 4Å: Chain I: K.201, N.203, I.246, H.320 Chain K: T.19, W.55, S.57, S.58, A.59, F.63, R.64, G.65, V.67, L.68, I.69, S.70, A.71, V.72, D.73, L.74, I.81, S.82, S.83, E.85 3 PLIP interactions: 3 interactions with chain K Hydrogen bonds: K:D.73, K:A.71, K:S.57, K:A.59, K:G.65 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.49: 24 residues within 4Å: Chain O: K.201, N.203, I.246, H.320 Chain Q: T.19, W.55, S.57, S.58, A.59, F.63, R.64, G.65, V.67, L.68, I.69, S.70, A.71, V.72, D.73, L.74, I.81, S.82, S.83, E.85 3 PLIP interactions: 3 interactions with chain Q Hydrogen bonds: Q:D.73, Q:A.71, Q:S.57, Q:A.59, Q:G.65

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.14: 7 residues within 4Å: Chain D: N.113 Chain F: N.32, Y.50, R.51, A.53, A.54, L.55 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:Y.50 NAG-NAG-BMA-MAN.32: 7 residues within 4Å: Chain J: N.113 Chain L: N.32, Y.50, R.51, A.53, A.54, L.55 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:Y.50, L:Y.50 NAG-NAG-BMA-MAN.50: 7 residues within 4Å: Chain P: N.113 Chain R: N.32, Y.50, R.51, A.53, A.54, L.55 1 PLIP interactions: 1 interactions with chain R Hydrogen bonds: R:Y.50

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

NAG.15: 6 residues within 4Å: Chain C: T.98, Q.100, S.119, N.121, K.130, K.132 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.130 NAG.16: 1 residues within 4Å: Chain C: N.323 No protein-ligand interaction detected (PLIP) NAG.17: 5 residues within 4Å: Chain C: N.103, R.112, K.116, R.139, K.158 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.103, C:R.112, C:K.116, C:K.158, C:K.158, C:K.158 NAG.18: 2 residues within 4Å: Chain D: N.87, S.89 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.87, D:S.89 NAG.33: 6 residues within 4Å: Chain I: T.98, Q.100, S.119, N.121, K.130, K.132 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:K.130 NAG.34: 1 residues within 4Å: Chain I: N.323 No protein-ligand interaction detected (PLIP) NAG.35: 5 residues within 4Å: Chain I: N.103, R.112, K.116, R.139, K.158 6 PLIP interactions: 6 interactions with chain I Hydrogen bonds: I:N.103, I:R.112, I:K.116, I:K.158, I:K.158, I:K.158 NAG.36: 2 residues within 4Å: Chain J: N.87, S.89 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:N.87, J:S.89 NAG.51: 6 residues within 4Å: Chain O: T.98, Q.100, S.119, N.121, K.130, K.132 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:K.130 NAG.52: 1 residues within 4Å: Chain O: N.323 No protein-ligand interaction detected (PLIP) NAG.53: 5 residues within 4Å: Chain O: N.103, R.112, K.116, R.139, K.158 6 PLIP interactions: 6 interactions with chain O Hydrogen bonds: O:N.103, O:R.112, O:K.116, O:K.158, O:K.158, O:K.158 NAG.54: 2 residues within 4Å: Chain P: N.87, S.89 2 PLIP interactions: 2 interactions with chain P Hydrogen bonds: P:N.87, P:S.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kong, L. et al., Uncleaved prefusion-optimized gp140 trimers derived from analysis of HIV-1 envelope metastability. Nat Commun (2016)

Release Date

2016-07-13

Peptides

broadly neutralizing antibody PGT128 heavy chain: AGM
broadly neutralizing antibody PGT128 light chain: BHN
gp120: CIO
gp41: DJP
broadly neutralizing antibody 8ANC195 heavy chain: EKQ
broadly neutralizing antibody 8ANC195 light chain: FLR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

G
A

M
A

B
B

H
B

N
B

C
C

I
C

O
C

D
D

J
D

P
D

E
E

K
E

Q
E

F
F

L
F

R
F

broadly neutralizing antibody PGT128 heavy chain

broadly neutralizing antibody PGT128 light chain

gp120

gp41

broadly neutralizing antibody 8ANC195 heavy chain

broadly neutralizing antibody 8ANC195 light chain

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