SMTL ID : 5fyj.1

Crystal Structure at 3.4 A Resolution of Fully Glycosylated HIV-1 Clade G X1193.c1 SOSIP.664 Prefusion Env Trimer in Complex with Broadly Neutralizing Antibodies PGT122, 35O22 and VRC01

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.11 Å

Oligo State

hetero-3-3-3-3-3-3-6-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: 3 residues within 4Å: Chain A: N.100, S.102, H.130 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain A: N.105, K.106, E.110 Chain C: G.59 Ligands: NAG-NAG-BMA.3, NAG-NAG-BMA.3 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: R.122, E.123, N.126 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 2 residues within 4Å: Chain D: N.434 Ligands: NAG-NAG-BMA.18 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 3 residues within 4Å: Chain I: N.100, S.102, H.130 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 6 residues within 4Å: Chain I: N.105, K.106, E.110 Chain K: G.59 Ligands: NAG-NAG-BMA.35, NAG-NAG-BMA.35 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 3 residues within 4Å: Chain I: R.122, E.123, N.126 No protein-ligand interaction detected (PLIP) NAG-NAG.54: 2 residues within 4Å: Chain L: N.434 Ligands: NAG-NAG-BMA.50 No protein-ligand interaction detected (PLIP) NAG-NAG.65: 3 residues within 4Å: Chain Q: N.100, S.102, H.130 No protein-ligand interaction detected (PLIP) NAG-NAG.66: 6 residues within 4Å: Chain Q: N.105, K.106, E.110 Chain S: G.59 Ligands: NAG-NAG-BMA.67, NAG-NAG-BMA.67 No protein-ligand interaction detected (PLIP) NAG-NAG.68: 3 residues within 4Å: Chain Q: R.122, E.123, N.126 No protein-ligand interaction detected (PLIP) NAG-NAG.86: 2 residues within 4Å: Chain T: N.434 Ligands: NAG-NAG-BMA.82 No protein-ligand interaction detected (PLIP)

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.3: 10 residues within 4Å: Chain A: E.110, N.114, L.115, E.119, E.123 Chain B: Q.1, L.108 Chain C: P.58 Ligands: NAG-NAG.2, NAG-NAG.2 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.1 NAG-NAG-BMA.9: 5 residues within 4Å: Chain D: R.169, N.174, V.175 Chain G: Y.190 Chain T: R.285 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:R.134 NAG-NAG-BMA.18: 2 residues within 4Å: Chain D: N.331 Ligands: NAG-NAG.22 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.35: 10 residues within 4Å: Chain I: E.110, N.114, L.115, E.119, E.123 Chain J: Q.1, L.108 Chain K: P.58 Ligands: NAG-NAG.34, NAG-NAG.34 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:Q.1 NAG-NAG-BMA.41: 5 residues within 4Å: Chain D: R.285 Chain L: R.169, N.174, V.175 Chain O: Y.190 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:R.134 NAG-NAG-BMA.50: 2 residues within 4Å: Chain L: N.331 Ligands: NAG-NAG.54 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.67: 10 residues within 4Å: Chain Q: E.110, N.114, L.115, E.119, E.123 Chain R: Q.1, L.108 Chain S: P.58 Ligands: NAG-NAG.66, NAG-NAG.66 1 PLIP interactions: 1 interactions with chain R Hydrogen bonds: R:Q.1 NAG-NAG-BMA.73: 5 residues within 4Å: Chain L: R.285 Chain T: R.169, N.174, V.175 Chain W: Y.190 1 PLIP interactions: 1 interactions with chain W Hydrogen bonds: W:R.134 NAG-NAG-BMA.82: 2 residues within 4Å: Chain T: N.331 Ligands: NAG-NAG.86 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: 19 residues within 4Å: Chain A: S.17 Chain B: N.30, F.31, H.33, W.50, S.52, Y.54, S.55, D.57, N.59, R.110, D.111, G.112, S.113, T.115 Chain C: H.95, N.96 Chain D: K.59, N.60 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:H.33, B:S.52, C:H.95, B:G.112, B:T.115 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.37: 19 residues within 4Å: Chain I: S.17 Chain J: N.30, F.31, H.33, W.50, S.52, Y.54, S.55, D.57, N.59, R.110, D.111, G.112, S.113, T.115 Chain K: H.95, N.96 Chain L: K.59, N.60 3 PLIP interactions: 2 interactions with chain J, 1 interactions with chain K Hydrogen bonds: J:H.33, J:S.52, J:G.112, J:T.115, K:H.95 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.69: 19 residues within 4Å: Chain Q: S.17 Chain R: N.30, F.31, H.33, W.50, S.52, Y.54, S.55, D.57, N.59, R.110, D.111, G.112, S.113, T.115 Chain S: H.95, N.96 Chain T: K.59, N.60 3 PLIP interactions: 2 interactions with chain R, 1 interactions with chain S Hydrogen bonds: R:H.33, R:S.52, R:G.112, R:T.115, S:H.95

6 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: 5 residues within 4Å: Chain D: V.106, N.131, Y.148, L.150 Chain F: E.20 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.12: 17 residues within 4Å: Chain D: S.37, P.183, K.184, V.185, T.186, D.188, P.189, V.231, N.239, R.281, R.354, C.414, R.415, S.416, R.417 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.21, NAG-NAG-BMA-MAN-MAN-MAN-MAN.21 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.354, D:R.415, D:R.354 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.38: 5 residues within 4Å: Chain L: V.106, N.131, Y.148, L.150 Chain N: E.20 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.44: 17 residues within 4Å: Chain L: S.37, P.183, K.184, V.185, T.186, D.188, P.189, V.231, N.239, R.281, R.354, C.414, R.415, S.416, R.417 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.53, NAG-NAG-BMA-MAN-MAN-MAN-MAN.53 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:R.354, L:R.415, L:R.354 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.70: 5 residues within 4Å: Chain T: V.106, N.131, Y.148, L.150 Chain V: E.20 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.76: 17 residues within 4Å: Chain T: S.37, P.183, K.184, V.185, T.186, D.188, P.189, V.231, N.239, R.281, R.354, C.414, R.415, S.416, R.417 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.85, NAG-NAG-BMA-MAN-MAN-MAN-MAN.85 1 PLIP interactions: 1 interactions with chain T Hydrogen bonds: T:R.354, T:R.415, T:R.354

9 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.7: 10 residues within 4Å: Chain D: T.100, N.135, K.146, K.164 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.8, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.39, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.39, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.39, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.71, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.71 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.8: 2 residues within 4Å: Chain D: N.165 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.7 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.16: 19 residues within 4Å: Chain D: T.274, H.306, N.308, N.382, T.384 Chain E: R.103, I.104, Y.105, G.106, V.107, V.108 Chain F: S.24, N.44, N.45, P.60, G.61, S.62 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.20, NAG-NAG-BMA-MAN-MAN-MAN-MAN.21 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:V.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.39: 10 residues within 4Å: Chain L: T.100, N.135, K.146, K.164 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.7, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.7, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.40, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.71, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.71, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.71 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.40: 2 residues within 4Å: Chain L: N.165 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.39 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.48: 19 residues within 4Å: Chain L: T.274, H.306, N.308, N.382, T.384 Chain M: R.103, I.104, Y.105, G.106, V.107, V.108 Chain N: S.24, N.44, N.45, P.60, G.61, S.62 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.52, NAG-NAG-BMA-MAN-MAN-MAN-MAN.53 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:V.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.71: 10 residues within 4Å: Chain T: T.100, N.135, K.146, K.164 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.7, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.7, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.7, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.39, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.39, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.72 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.72: 2 residues within 4Å: Chain T: N.165 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.71 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.80: 19 residues within 4Å: Chain T: T.274, H.306, N.308, N.382, T.384 Chain U: R.103, I.104, Y.105, G.106, V.107, V.108 Chain V: S.24, N.44, N.45, P.60, G.61, S.62 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.84, NAG-NAG-BMA-MAN-MAN-MAN-MAN.85 1 PLIP interactions: 1 interactions with chain U Hydrogen bonds: U:V.108

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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.10: 4 residues within 4Å: Chain B: K.23 Chain D: N.211 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.13, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.13 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.42: 4 residues within 4Å: Chain J: K.23 Chain L: N.211 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.45, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.45 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.74: 4 residues within 4Å: Chain R: K.23 Chain T: N.211 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.77, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.77 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-(1-3)-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.11: 4 residues within 4Å: Chain D: R.206, K.208, N.218 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.14 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.43: 4 residues within 4Å: Chain L: R.206, K.208, N.218 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.46 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.75: 4 residues within 4Å: Chain T: R.206, K.208, N.218 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.78 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- 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)]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.13: 10 residues within 4Å: Chain D: N.253 Chain H: Y.28, G.29, S.30, R.64, W.65, G.66, P.67 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.10, NAG-NAG-BMA-MAN-MAN-MAN.10 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.45: 10 residues within 4Å: Chain L: N.253 Chain P: Y.28, G.29, S.30, R.64, W.65, G.66, P.67 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.42, NAG-NAG-BMA-MAN-MAN-MAN.42 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.77: 10 residues within 4Å: Chain T: N.253 Chain X: Y.28, G.29, S.30, R.64, W.65, G.66, P.67 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.74, NAG-NAG-BMA-MAN-MAN-MAN.74 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[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-MAN-MAN-MAN-MAN.14: 7 residues within 4Å: Chain D: A.268, N.270, E.313, R.415 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.11, NAG-NAG-BMA-MAN-MAN-MAN-MAN.17, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.20 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.46: 7 residues within 4Å: Chain L: A.268, N.270, E.313, R.415 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.43, NAG-NAG-BMA-MAN-MAN-MAN-MAN.49, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.52 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.78: 7 residues within 4Å: Chain T: A.268, N.270, E.313, R.415 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.75, NAG-NAG-BMA-MAN-MAN-MAN-MAN.81, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.84 No protein-ligand interaction detected (PLIP)

9 x NAG- NAG- BMA- MAN- MAN- MAN: 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.15: 3 residues within 4Å: Chain D: N.278, I.299 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.21 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.23: 3 residues within 4Å: Chain E: Q.5, N.23, L.77 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.24: 4 residues within 4Å: Chain H: I.20, S.63, R.64, N.70 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.47: 3 residues within 4Å: Chain L: N.278, I.299 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.53 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.55: 3 residues within 4Å: Chain M: Q.5, N.23, L.77 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.56: 4 residues within 4Å: Chain P: I.20, S.63, R.64, N.70 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.79: 3 residues within 4Å: Chain T: N.278, I.299 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.85 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.87: 3 residues within 4Å: Chain U: Q.5, N.23, L.77 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.88: 4 residues within 4Å: Chain X: I.20, S.63, R.64, N.70 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.17: 6 residues within 4Å: Chain D: T.267, E.313, D.316, M.317, N.320 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.14 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.49: 6 residues within 4Å: Chain L: T.267, E.313, D.316, M.317, N.320 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.46 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.81: 6 residues within 4Å: Chain T: T.267, E.313, D.316, M.317, N.320 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.78 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: 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)-[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-MAN-MAN.19: 9 residues within 4Å: Chain D: T.118, N.120, D.124, Y.125, T.347, N.361, S.363 Chain G: G.181 Ligands: NAG.28 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain G Hydrogen bonds: D:D.124, G:G.181 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.51: 9 residues within 4Å: Chain L: T.118, N.120, D.124, Y.125, T.347, N.361, S.363 Chain O: G.181 Ligands: NAG.60 2 PLIP interactions: 1 interactions with chain L, 1 interactions with chain O Hydrogen bonds: L:D.124, O:G.181 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.83: 9 residues within 4Å: Chain T: T.118, N.120, D.124, Y.125, T.347, N.361, S.363 Chain W: G.181 Ligands: NAG.92 2 PLIP interactions: 1 interactions with chain T, 1 interactions with chain W Hydrogen bonds: T:D.124, W:G.181

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: 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)-[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-MAN-MAN-MAN-MAN-MAN.20: 7 residues within 4Å: Chain D: T.272, N.308, N.382 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.14, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.16, NAG-NAG-BMA-MAN-MAN-MAN-MAN.21, NAG-NAG-BMA-MAN-MAN-MAN-MAN.21 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:T.272 Hydrogen bonds: D:R.415 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.52: 7 residues within 4Å: Chain L: T.272, N.308, N.382 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.46, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.48, NAG-NAG-BMA-MAN-MAN-MAN-MAN.53, NAG-NAG-BMA-MAN-MAN-MAN-MAN.53 2 PLIP interactions: 2 interactions with chain L Hydrophobic interactions: L:T.272 Hydrogen bonds: L:R.415 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.84: 7 residues within 4Å: Chain T: T.272, N.308, N.382 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.78, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.80, NAG-NAG-BMA-MAN-MAN-MAN-MAN.85, NAG-NAG-BMA-MAN-MAN-MAN-MAN.85 2 PLIP interactions: 2 interactions with chain T Hydrophobic interactions: T:T.272 Hydrogen bonds: T:R.415

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-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.21: 7 residues within 4Å: Chain D: P.276, N.411 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.12, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.12, NAG-NAG-BMA-MAN-MAN-MAN.15, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.16, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.20 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.53: 7 residues within 4Å: Chain L: P.276, N.411 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.44, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.44, NAG-NAG-BMA-MAN-MAN-MAN.47, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.48, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.52 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.85: 7 residues within 4Å: Chain T: P.276, N.411 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.76, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.76, NAG-NAG-BMA-MAN-MAN-MAN.79, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.80, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.84 No protein-ligand interaction detected (PLIP)

9 x CIT: CITRIC ACID(Non-functional Binders)

CIT.25: 8 residues within 4Å: Chain A: R.74, Q.77, D.78 Chain D: K.461, K.463, P.464, L.465 Chain Q: R.46 7 PLIP interactions: 3 interactions with chain D, 1 interactions with chain Q, 3 interactions with chain A Salt bridges: D:K.461, D:K.463, D:K.463, Q:R.46, A:R.74 Hydrogen bonds: A:R.74, A:D.78 CIT.29: 8 residues within 4Å: Chain D: W.68, E.252, A.258, K.259, D.448, R.451 Chain G: K.167, D.218 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain G Hydrogen bonds: D:K.259, D:T.260 Salt bridges: D:K.259, D:K.259, D:R.451, D:R.451, G:K.167 CIT.31: 8 residues within 4Å: Chain D: H.77, I.81, W.396, V.399, D.445, R.447 Chain G: D.146, R.169 12 PLIP interactions: 9 interactions with chain D, 3 interactions with chain G Hydrophobic interactions: D:I.81, D:V.399 Hydrogen bonds: D:H.77, D:D.445, D:M.446, D:R.447, D:R.447, G:R.169 Salt bridges: D:H.77, D:R.447, G:R.169, G:R.169 CIT.57: 8 residues within 4Å: Chain A: R.46 Chain I: R.74, Q.77, D.78 Chain L: K.461, K.463, P.464, L.465 7 PLIP interactions: 3 interactions with chain I, 3 interactions with chain L, 1 interactions with chain A Hydrogen bonds: I:R.74, I:D.78 Salt bridges: I:R.74, L:K.461, L:K.463, L:K.463, A:R.46 CIT.61: 8 residues within 4Å: Chain L: W.68, E.252, A.258, K.259, D.448, R.451 Chain O: K.167, D.218 7 PLIP interactions: 6 interactions with chain L, 1 interactions with chain O Hydrogen bonds: L:K.259, L:T.260 Salt bridges: L:K.259, L:K.259, L:R.451, L:R.451, O:K.167 CIT.63: 8 residues within 4Å: Chain L: H.77, I.81, W.396, V.399, D.445, R.447 Chain O: D.146, R.169 12 PLIP interactions: 9 interactions with chain L, 3 interactions with chain O Hydrophobic interactions: L:I.81, L:V.399 Hydrogen bonds: L:H.77, L:D.445, L:M.446, L:R.447, L:R.447, O:R.169 Salt bridges: L:H.77, L:R.447, O:R.169, O:R.169 CIT.89: 8 residues within 4Å: Chain I: R.46 Chain Q: R.74, Q.77, D.78 Chain T: K.461, K.463, P.464, L.465 7 PLIP interactions: 1 interactions with chain I, 3 interactions with chain T, 3 interactions with chain Q Salt bridges: I:R.46, T:K.461, T:K.463, T:K.463, Q:R.74 Hydrogen bonds: Q:R.74, Q:D.78 CIT.93: 8 residues within 4Å: Chain T: W.68, E.252, A.258, K.259, D.448, R.451 Chain W: K.167, D.218 7 PLIP interactions: 6 interactions with chain T, 1 interactions with chain W Hydrogen bonds: T:K.259, T:T.260 Salt bridges: T:K.259, T:K.259, T:R.451, T:R.451, W:K.167 CIT.95: 8 residues within 4Å: Chain T: H.77, I.81, W.396, V.399, D.445, R.447 Chain W: D.146, R.169 12 PLIP interactions: 9 interactions with chain T, 3 interactions with chain W Hydrophobic interactions: T:I.81, T:V.399 Hydrogen bonds: T:H.77, T:D.445, T:M.446, T:R.447, T:R.447, W:R.169 Salt bridges: T:H.77, T:R.447, W:R.169, W:R.169

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

EDO.26: 3 residues within 4Å: Chain A: R.122 Chain B: T.79, S.80 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.122, B:S.80 EDO.30: 3 residues within 4Å: Chain D: D.29, P.53, H.193 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.227 EDO.58: 3 residues within 4Å: Chain I: R.122 Chain J: T.79, S.80 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain J Hydrogen bonds: I:R.122, J:S.80 EDO.62: 3 residues within 4Å: Chain L: D.29, P.53, H.193 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:G.227 EDO.90: 3 residues within 4Å: Chain Q: R.122 Chain R: T.79, S.80 2 PLIP interactions: 1 interactions with chain Q, 1 interactions with chain R Hydrogen bonds: Q:R.122, R:S.80 EDO.94: 3 residues within 4Å: Chain T: D.29, P.53, H.193 1 PLIP interactions: 1 interactions with chain T Hydrogen bonds: T:G.227

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

NAG.27: 5 residues within 4Å: Chain D: N.105, Q.128, L.129, K.130, R.153 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.105, D:Q.128, D:K.130, D:K.130 NAG.28: 2 residues within 4Å: Chain D: N.120 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.19 No protein-ligand interaction detected (PLIP) NAG.32: 5 residues within 4Å: Chain D: G.364, N.367, S.369, I.383, T.384 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.367, D:T.384 NAG.59: 5 residues within 4Å: Chain L: N.105, Q.128, L.129, K.130, R.153 4 PLIP interactions: 4 interactions with chain L Hydrogen bonds: L:N.105, L:Q.128, L:K.130, L:K.130 NAG.60: 2 residues within 4Å: Chain L: N.120 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.51 No protein-ligand interaction detected (PLIP) NAG.64: 5 residues within 4Å: Chain L: G.364, N.367, S.369, I.383, T.384 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:N.367, L:T.384 NAG.91: 5 residues within 4Å: Chain T: N.105, Q.128, L.129, K.130, R.153 4 PLIP interactions: 4 interactions with chain T Hydrogen bonds: T:N.105, T:Q.128, T:K.130, T:K.130 NAG.92: 2 residues within 4Å: Chain T: N.120 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.83 No protein-ligand interaction detected (PLIP) NAG.96: 5 residues within 4Å: Chain T: G.364, N.367, S.369, I.383, T.384 2 PLIP interactions: 2 interactions with chain T Hydrogen bonds: T:N.367, T:T.384

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stewart-Jones, G.B.E. et al., Trimeric HIV-1-Env Structures Define Glycan Shields from Clades A, B and G. Cell(Cambridge,Mass.) (2016)

Release Date

2016-04-27

Peptides

GP41 ENV ECTODOMAIN: AIQ
35O22: BJR
35O22: CKS
GP120 ENV ECTODOMAIN: DLT
PGT122: EMU
PGT122: FNV
VRC01: GHOPWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

I
B

Q
B

B
D

J
D

R
D

C
E

K
E

S
E

D
G

L
G

T
G

E
H

M
H

U
H

F
L

N
L

V
L

G
U

H
V

O
U

P
V

W
U

X
V

GP41 ENV ECTODOMAIN

35O22

35O22

GP120 ENV ECTODOMAIN

PGT122

PGT122

VRC01

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