SMTL ID : 6u59.1

HIV-1 B41 SOSIP.664 in complex with rabbit antibody 13B

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

33 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: V.139, N.165, Y.182, L.184, D.336 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.182 NAG-NAG.2: 2 residues within 4Å: Chain A: T.133, N.169 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.250, S.252, I.293, Q.367 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.292, T.294, D.295 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.294 NAG-NAG.5: 6 residues within 4Å: Chain A: E.309, N.311, N.347, I.348, S.349 Ligands: NAG-NAG.13 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: I.374, N.376, R.480 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain A: N.400, T.402 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain A: P.403, N.406, Y.417, E.422, I.425 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.422 NAG-NAG.10: 4 residues within 4Å: Chain A: R.268, N.278, N.459 Ligands: NAG-NAG-BMA-MAN.11 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 8 residues within 4Å: Chain A: E.88, V.90, N.245, K.247, N.257 Chain D: D.28, Y.29, Y.95 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain A: Q.423, N.424 Ligands: NAG-NAG.5, NAG-NAG-BMA.6, NAG-NAG-BMA.6 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain E: V.139, N.165, Y.182, L.184, D.336 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.182 NAG-NAG.15: 2 residues within 4Å: Chain E: T.133, N.169 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain E: N.250, S.252, I.293, Q.367 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain E: N.292, T.294, D.295 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:T.294 NAG-NAG.18: 6 residues within 4Å: Chain E: E.309, N.311, N.347, I.348, S.349 Ligands: NAG-NAG.26 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain E: I.374, N.376, R.480 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 2 residues within 4Å: Chain E: N.400, T.402 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 5 residues within 4Å: Chain E: P.403, N.406, Y.417, E.422, I.425 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.422 NAG-NAG.23: 4 residues within 4Å: Chain E: R.268, N.278, N.459 Ligands: NAG-NAG-BMA-MAN.24 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 8 residues within 4Å: Chain E: E.88, V.90, N.245, K.247, N.257 Chain H: D.28, Y.29, Y.95 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 5 residues within 4Å: Chain E: Q.423, N.424 Ligands: NAG-NAG.18, NAG-NAG-BMA.19, NAG-NAG-BMA.19 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 5 residues within 4Å: Chain I: V.139, N.165, Y.182, L.184, D.336 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:Y.182 NAG-NAG.28: 2 residues within 4Å: Chain I: T.133, N.169 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 4 residues within 4Å: Chain I: N.250, S.252, I.293, Q.367 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 3 residues within 4Å: Chain I: N.292, T.294, D.295 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:T.294 NAG-NAG.31: 6 residues within 4Å: Chain I: E.309, N.311, N.347, I.348, S.349 Ligands: NAG-NAG.39 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 3 residues within 4Å: Chain I: I.374, N.376, R.480 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 2 residues within 4Å: Chain I: N.400, T.402 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 5 residues within 4Å: Chain I: P.403, N.406, Y.417, E.422, I.425 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:E.422 NAG-NAG.36: 4 residues within 4Å: Chain I: R.268, N.278, N.459 Ligands: NAG-NAG-BMA-MAN.37 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 8 residues within 4Å: Chain I: E.88, V.90, N.245, K.247, N.257 Chain L: D.28, Y.29, Y.95 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 5 residues within 4Å: Chain I: Q.423, N.424 Ligands: NAG-NAG.31, NAG-NAG-BMA.32, NAG-NAG-BMA.32 No protein-ligand interaction detected (PLIP)

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.6: 7 residues within 4Å: Chain A: W.155, E.156, T.313, H.345, N.347, T.426 Ligands: NAG-NAG.13 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.156 NAG-NAG-BMA.19: 7 residues within 4Å: Chain E: W.155, E.156, T.313, H.345, N.347, T.426 Ligands: NAG-NAG.26 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:E.156 NAG-NAG-BMA.32: 7 residues within 4Å: Chain I: W.155, E.156, T.313, H.345, N.347, T.426 Ligands: NAG-NAG.39 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:E.156

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.11: 8 residues within 4Å: Chain A: V.70, E.227, P.228, L.277, N.278, S.457, S.458 Ligands: NAG-NAG.10 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.24: 8 residues within 4Å: Chain E: V.70, E.227, P.228, L.277, N.278, S.457, S.458 Ligands: NAG-NAG.23 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.37: 8 residues within 4Å: Chain I: V.70, E.227, P.228, L.277, N.278, S.457, S.458 Ligands: NAG-NAG.36 No protein-ligand interaction detected (PLIP)

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

NAG.40: 3 residues within 4Å: Chain A: G.92, N.93 Chain B: A.21 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain A: R.208, N.213, T.214 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain A: N.317, I.338, Q.453 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain A: K.350, N.354, T.414, Y.417 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain A: P.369, N.370 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain A: N.370, T.372, N.410 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain B: N.105, K.106 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain B: N.114 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain B: E.123, N.126 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain B: N.100, S.102, H.130 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain E: G.92, N.93 Chain F: A.21 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain E: R.208, N.213, T.214 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain E: N.317, I.338, Q.453 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain E: K.350, N.354, T.414, Y.417 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain E: P.369, N.370 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain E: N.370, T.372, N.410 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain F: N.105, K.106 Ligand excluded by PLIP NAG.57: 1 residues within 4Å: Chain F: N.114 Ligand excluded by PLIP NAG.58: 2 residues within 4Å: Chain F: E.123, N.126 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain F: N.100, S.102, H.130 Ligand excluded by PLIP NAG.60: 3 residues within 4Å: Chain I: G.92, N.93 Chain J: A.21 Ligand excluded by PLIP NAG.61: 3 residues within 4Å: Chain I: R.208, N.213, T.214 Ligand excluded by PLIP NAG.62: 3 residues within 4Å: Chain I: N.317, I.338, Q.453 Ligand excluded by PLIP NAG.63: 4 residues within 4Å: Chain I: K.350, N.354, T.414, Y.417 Ligand excluded by PLIP NAG.64: 2 residues within 4Å: Chain I: P.369, N.370 Ligand excluded by PLIP NAG.65: 3 residues within 4Å: Chain I: N.370, T.372, N.410 Ligand excluded by PLIP NAG.66: 2 residues within 4Å: Chain J: N.105, K.106 Ligand excluded by PLIP NAG.67: 1 residues within 4Å: Chain J: N.114 Ligand excluded by PLIP NAG.68: 2 residues within 4Å: Chain J: E.123, N.126 Ligand excluded by PLIP NAG.69: 3 residues within 4Å: Chain J: N.100, S.102, H.130 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Y.R. et al., Autologous Antibody Responses to an HIV Envelope Glycan Hole Are Not Easily Broadened in Rabbits. J.Virol. (2020)

Release Date

2020-01-29

Peptides

SOSIP.664 gp120,SOSIP.664 gp120: AEI
SOSIP.664 gp41: BFJ
rabbit antibody 13B Fragment antigen binding light chain: CGK
rabbit antibody 13B Fragment antigen binding heavy chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
C

I
G

B
B

F
D

J
I

C
L

G
E

K
J

D
H

H
F

L
K

SOSIP.664 gp120,SOSIP.664 gp120

SOSIP.664 gp41

rabbit antibody 13B Fragment antigen binding light chain

rabbit antibody 13B Fragment antigen binding heavy chain

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