SMTL ID : 6crq.1

Glutaraldehyde-treated BG505 SOSIP.664 Env in complex with PGV04 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

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.1: 9 residues within 4Å: Chain A: E.33, E.180, V.223, L.230, N.231, C.412, V.413, S.414 Ligands: NAG-NAG.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.33, A:E.33, A:V.413 Hydrophobic interactions: A:V.413 NAG-NAG-BMA-MAN.13: 7 residues within 4Å: Chain E: E.33, E.180, V.223, N.231, V.413, S.414 Ligands: NAG-NAG.14 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.25: 8 residues within 4Å: Chain I: E.33, P.181, V.223, L.230, N.231, V.413, S.414 Ligands: NAG-NAG.26 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:E.33, I:E.33

27 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: 4 residues within 4Å: Chain A: P.260, V.413, N.415 Ligands: NAG-NAG-BMA-MAN.1 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: Q.262, N.264 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.354, S.356 Ligands: NAG-NAG.6, NAG-NAG.6 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: N.331, S.332 Ligands: NAG-NAG.5 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 6 residues within 4Å: Chain A: C.100, N.102, M.111, N.157, K.158, Y.160 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain A: V.103, T.104, N.117, Y.134, L.136 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.134 NAG-NAG.10: 3 residues within 4Å: Chain A: N.269, N.270, I.291 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain A: N.57 Chain B: G.13, G.16, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain A: N.264, T.266, H.298, N.300 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain E: N.231, P.260, V.413, N.415 Ligands: NAG-NAG-BMA-MAN.13 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain E: Q.262, N.264, N.300 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain E: N.354, S.356 Ligands: NAG-NAG.18, NAG-NAG.18 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain E: N.331, S.332, N.354 Ligands: NAG-NAG.17 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 8 residues within 4Å: Chain E: C.100, T.101, N.102, M.111, Q.144, N.157, K.158, Y.160 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 4 residues within 4Å: Chain E: V.103, N.117, Y.134, L.136 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.134 NAG-NAG.22: 3 residues within 4Å: Chain E: N.269, N.270, I.291 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain E: N.57 Chain F: L.9, G.16, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain E: N.264, T.266, H.298, N.300 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 5 residues within 4Å: Chain I: P.260, V.413, S.414, N.415 Ligands: NAG-NAG-BMA-MAN.25 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 4 residues within 4Å: Chain I: Q.262, N.264, N.300, S.302 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 4 residues within 4Å: Chain I: N.354, S.356 Ligands: NAG-NAG.30, NAG-NAG.30 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 3 residues within 4Å: Chain I: N.331, S.332 Ligands: NAG-NAG.29 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 7 residues within 4Å: Chain I: C.100, N.102, M.111, Q.144, N.157, K.158, Y.160 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 5 residues within 4Å: Chain I: T.104, N.117, Y.134, L.136, D.289 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 3 residues within 4Å: Chain I: N.269, N.270, I.291 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 3 residues within 4Å: Chain I: N.57 Chain J: G.16, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 4 residues within 4Å: Chain I: N.264, T.266, H.298, N.300 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: 7 residues within 4Å: Chain A: N.245 Chain C: G.107 Chain D: Y.28, G.29, H.30, Q.64, F.65 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.15: 8 residues within 4Å: Chain E: N.245, I.246 Chain H: Y.28, G.29, H.30, Q.64, F.65, G.66 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:G.66 NAG-NAG-BMA-MAN.27: 7 residues within 4Å: Chain I: N.245, T.247 Chain K: G.107 Chain L: Y.28, Q.64, F.65, G.66 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:G.66

3 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.7: 2 residues within 4Å: Chain A: R.161, N.166 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 2 residues within 4Å: Chain E: R.161, N.166 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.31: 3 residues within 4Å: Chain I: R.161, N.166 Chain K: D.77 No protein-ligand interaction detected (PLIP)

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

NAG.37: 2 residues within 4Å: Chain A: Q.99, N.121 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain A: K.201, N.203 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain A: K.303, N.307, W.363 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain B: K.122, E.123, I.124, S.125, N.126 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain B: N.105, R.106, N.107 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain B: P.98, N.100, S.102, W.103, L.134 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain E: Q.99, S.119, F.120, N.121 Ligand excluded by PLIP NAG.44: 5 residues within 4Å: Chain E: D.199, K.201, F.202, N.203, T.205 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain E: K.303, N.307 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain F: K.122, N.126 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain F: N.107 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain F: P.98, N.100 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain I: Q.99, S.119, N.121 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain I: D.199, K.201, F.202, N.203 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain I: K.303, N.307, W.363 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain J: E.123, N.126, Y.127 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain J: N.105, R.106, N.107 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain J: P.98, N.100 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schiffner, T. et al., Structural and immunologic correlates of chemically stabilized HIV-1 envelope glycoproteins. PLoS Pathog. (2018)

Release Date

2018-04-18

Peptides

Envelope glycoprotein gp160: AEI
Envelope glycoprotein gp160: BFJ
PGV04 VH: CGK
PGV04 VL: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
B

I
F

B
C

F
G

J
H

C
D

G
I

K
J

D
E

H
K

L
L

Envelope glycoprotein gp160

Envelope glycoprotein gp160

PGV04 VH

PGV04 VL

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