SMTL ID : 7l6o.1

Cryo-EM structure of HIV-1 Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

27 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: 5 residues within 4Å: Chain A: K.320, N.322, Q.323, G.353, R.427 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 7 residues within 4Å: Chain A: Q.323, S.348, N.349, N.352, G.353 Ligands: NAG-NAG-BMA.7, NAG-NAG-BMA.10 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 8 residues within 4Å: Chain A: E.53, V.55, K.189, N.191, D.192, E.193, N.203, S.205 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.53, A:N.191 NAG-NAG-BMA.6: 11 residues within 4Å: Chain A: A.104, T.105, V.106, N.116, S.118, K.131, E.132, Y.133, L.135, D.282, I.283 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 5 residues within 4Å: Chain A: Q.323, T.333, N.346, S.348 Ligands: NAG-NAG-BMA.2 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 6 residues within 4Å: Chain A: V.257, T.259, H.291, N.293, T.371, T.373 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 12 residues within 4Å: Chain A: E.296, W.299, N.300, L.303, Q.304, Y.321, N.352, G.353, T.354, Y.355, I.360 Ligands: NAG-NAG-BMA.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.353 NAG-NAG-BMA.12: 6 residues within 4Å: Chain A: T.98, I.100, S.118, F.119, N.120, K.131 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 7 residues within 4Å: Chain A: V.142, P.143, R.154, I.156, N.159, T.160, D.328 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 5 residues within 4Å: Chain C: K.320, N.322, Q.323, G.353, R.427 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 6 residues within 4Å: Chain C: Q.323, S.348, N.352, G.353 Ligands: NAG-NAG-BMA.20, NAG-NAG-BMA.23 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 8 residues within 4Å: Chain C: E.53, V.55, K.189, N.191, D.192, E.193, N.203, S.205 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.53, C:N.191 NAG-NAG-BMA.19: 10 residues within 4Å: Chain C: A.104, T.105, V.106, N.116, S.118, K.131, Y.133, L.135, D.282, I.283 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 5 residues within 4Å: Chain C: Q.323, T.333, N.346, S.348 Ligands: NAG-NAG-BMA.15 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 6 residues within 4Å: Chain C: V.257, T.259, H.291, N.293, T.371, T.373 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 12 residues within 4Å: Chain C: E.296, W.299, N.300, L.303, Q.304, Y.321, N.352, G.353, T.354, Y.355, I.360 Ligands: NAG-NAG-BMA.15 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.353 NAG-NAG-BMA.25: 6 residues within 4Å: Chain C: T.98, I.100, S.118, F.119, N.120, K.131 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.26: 6 residues within 4Å: Chain C: V.142, P.143, R.154, I.156, N.159, T.160 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 5 residues within 4Å: Chain E: K.320, N.322, Q.323, G.353, R.427 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.28: 7 residues within 4Å: Chain E: Q.323, S.348, N.349, N.352, G.353 Ligands: NAG-NAG-BMA.33, NAG-NAG-BMA.36 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.30: 6 residues within 4Å: Chain E: E.53, V.55, N.191, D.192, E.193, N.203 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:E.53, E:N.191 NAG-NAG-BMA.32: 10 residues within 4Å: Chain E: A.104, T.105, V.106, N.116, S.118, K.131, E.132, Y.133, L.135, D.282 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.33: 5 residues within 4Å: Chain E: Q.323, T.333, N.346, S.348 Ligands: NAG-NAG-BMA.28 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.35: 7 residues within 4Å: Chain E: V.257, T.259, K.288, H.291, N.293, T.371, T.373 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.36: 12 residues within 4Å: Chain E: E.296, W.299, N.300, L.303, Q.304, Y.321, G.353, T.354, Y.355, I.360, N.363 Ligands: NAG-NAG-BMA.28 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:G.353 NAG-NAG-BMA.38: 5 residues within 4Å: Chain E: T.98, I.100, F.119, N.120, K.131 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.39: 7 residues within 4Å: Chain C: R.270 Chain E: V.142, P.143, R.154, I.156, N.159, T.160 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.3: 8 residues within 4Å: Chain A: W.66, N.196, G.197, T.198, R.235, S.236, E.237 Ligands: NAG.41 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain A: N.263, T.265, I.284 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain A: N.103, T.110, K.138 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 9 residues within 4Å: Chain C: W.66, N.196, G.197, T.198, P.200, R.235, S.236, E.237 Ligands: NAG.47 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain C: N.263, T.265, I.284 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 3 residues within 4Å: Chain C: N.103, T.110, K.138 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 7 residues within 4Å: Chain E: W.66, N.196, G.197, T.198, R.235, S.236, E.237 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 3 residues within 4Å: Chain E: N.263, T.265, I.284 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 3 residues within 4Å: Chain E: N.103, T.110, K.138 No protein-ligand interaction detected (PLIP)

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.5: 15 residues within 4Å: Chain A: T.171, E.173, P.174, V.216, L.223, N.224, F.336, N.337, C.338, G.339, C.403, R.404, S.405, N.406 Ligands: NAG.42 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.173, A:R.404 NAG-NAG-BMA-MAN-MAN.18: 15 residues within 4Å: Chain C: T.171, E.173, P.174, V.216, L.223, N.224, F.336, N.337, C.338, G.339, C.403, R.404, S.405, N.406 Ligands: NAG.48 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.404 NAG-NAG-BMA-MAN-MAN.31: 14 residues within 4Å: Chain E: T.171, E.173, P.174, V.216, L.223, N.224, F.336, N.337, G.339, C.403, R.404, S.405, N.406 Ligands: NAG.54 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:E.173, E:R.404

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

NAG.40: 3 residues within 4Å: Chain A: L.56, N.58 Chain B: S.10 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain A: N.238, T.240, N.241 Ligands: NAG-NAG.3 Ligand excluded by PLIP NAG.42: 7 residues within 4Å: Chain A: L.227, P.253, R.404, S.405, N.406 Ligands: NAG-NAG-BMA-MAN-MAN.5, NAG-NAG-BMA-MAN-MAN.5 Ligand excluded by PLIP NAG.43: 7 residues within 4Å: Chain A: R.260, P.261, N.262, G.399, N.400, I.401, T.402 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain B: N.93, S.95 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain B: S.118, N.119 Ligand excluded by PLIP NAG.46: 7 residues within 4Å: Chain C: L.56, G.57, N.58 Chain D: G.6, A.7, G.9, S.10 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain C: N.238, T.240, N.241 Ligands: NAG-NAG.16 Ligand excluded by PLIP NAG.48: 7 residues within 4Å: Chain C: L.227, P.253, R.404, S.405, N.406 Ligands: NAG-NAG-BMA-MAN-MAN.18, NAG-NAG-BMA-MAN-MAN.18 Ligand excluded by PLIP NAG.49: 8 residues within 4Å: Chain C: R.260, P.261, N.262, N.263, G.399, N.400, I.401, T.402 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain D: N.93, S.95, Y.120 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain D: S.118, N.119 Ligand excluded by PLIP NAG.52: 6 residues within 4Å: Chain E: L.56, G.57, N.58 Chain F: A.7, G.9, S.10 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain E: N.238, T.240, N.241 Ligand excluded by PLIP NAG.54: 7 residues within 4Å: Chain E: L.227, P.253, R.404, S.405, N.406 Ligands: NAG-NAG-BMA-MAN-MAN.31, NAG-NAG-BMA-MAN-MAN.31 Ligand excluded by PLIP NAG.55: 7 residues within 4Å: Chain E: R.260, P.261, N.262, G.399, N.400, I.401, T.402 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain F: N.93, S.95, Y.120 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain F: S.118, N.119 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Williams, W.B. et al., Fab-dimerized glycan-reactive antibodies are a structural category of natural antibodies. Cell (2021)

Release Date

2021-04-14

Peptides

CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 - gp120: ACE
CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 - gp41: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
a

C
c

E
e

B
b

D
d

F
f

CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 - gp120

CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 - gp41

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