SMTL ID : 6edu.1

B41 SOSIP.664 in complex with soluble CD4 (D1-D2), the co-receptor mimicking antibody 21c and the broadly neutralizing antibody 8ANC195

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 4.06 Å

Oligo State

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

Ligands

15 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: 9 residues within 4Å: Chain A: D.125, N.126 Chain R: W.108, S.109 Chain S: N.32, Y.50, R.51, A.53, A.54 2 PLIP interactions: 2 interactions with chain S Hydrogen bonds: S:Y.50, S:Y.50 NAG-NAG.2: 9 residues within 4Å: Chain B: D.125, N.126 Chain P: W.108, S.109 Chain Q: N.32, Y.50, R.51, A.53, A.54 2 PLIP interactions: 2 interactions with chain Q Hydrogen bonds: Q:Y.50, Q:Y.50 NAG-NAG.3: 9 residues within 4Å: Chain C: D.125, N.126 Chain T: W.108, S.109 Chain U: N.32, Y.50, R.51, A.53, A.54 2 PLIP interactions: 2 interactions with chain U Hydrogen bonds: U:Y.50, U:Y.50 NAG-NAG.4: 2 residues within 4Å: Chain D: N.245, N.257 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain D: N.400, T.402 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain D: N.347, Q.423, N.424 Ligands: NAG.32, NAG.33 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 9 residues within 4Å: Chain D: I.174, R.175, N.211, C.212, N.213 Chain L: N.101, Y.102, Y.103 Chain M: F.50 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain E: N.245, N.257 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain E: N.400, T.402 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 5 residues within 4Å: Chain E: N.347, Q.423, N.424 Ligands: NAG.40, NAG.41 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 9 residues within 4Å: Chain E: I.174, R.175, N.211, C.212, N.213 Chain N: N.101, Y.102 Chain O: F.50, Q.54 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:Q.54 NAG-NAG.18: 2 residues within 4Å: Chain F: N.245, N.257 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 2 residues within 4Å: Chain F: N.400, T.402 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 5 residues within 4Å: Chain F: N.347, Q.423, N.424 Ligands: NAG.48, NAG.49 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 10 residues within 4Å: Chain F: I.174, R.175, N.211, C.212, N.213 Chain J: N.101, Y.102 Chain K: F.50, Q.54, R.55 2 PLIP interactions: 1 interactions with chain J, 1 interactions with chain K Hydrogen bonds: J:N.101, K:Q.54

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.5: 17 residues within 4Å: Chain D: S.225, P.228, V.270, L.277, N.278, F.390, N.391, C.392, G.393, I.450, G.452, Q.453, R.455, C.456, S.457, S.458 Ligands: NAG.38 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.452, D:Q.453, D:Q.453 NAG-NAG-BMA-MAN-MAN.12: 17 residues within 4Å: Chain E: S.225, P.228, V.270, L.277, N.278, F.390, N.391, C.392, G.393, I.450, G.452, Q.453, R.455, C.456, S.457, S.458 Ligands: NAG.46 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:G.452, E:Q.453, E:Q.453 NAG-NAG-BMA-MAN-MAN.19: 17 residues within 4Å: Chain F: S.225, P.228, V.270, L.277, N.278, F.390, N.391, C.392, G.393, I.450, G.452, Q.453, R.455, C.456, S.457, S.458 Ligands: NAG.54 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:G.452, F:Q.453, F:Q.453

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.6: 8 residues within 4Å: Chain D: N.292, T.294, D.295 Chain R: Q.1, H.3, Y.25, G.26, N.28 1 PLIP interactions: 1 interactions with chain R Hydrogen bonds: R:Q.1 NAG-NAG-BMA-MAN-MAN.13: 8 residues within 4Å: Chain E: N.292, T.294, D.295 Chain T: Q.1, H.3, Y.25, G.26, N.28 1 PLIP interactions: 1 interactions with chain T Hydrogen bonds: T:Q.1, T:Q.1, T:Y.25 NAG-NAG-BMA-MAN-MAN.20: 9 residues within 4Å: Chain F: N.292, T.294, D.295 Chain P: Q.1, H.3, Y.25, G.26, V.27, N.28 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:Q.1, P:Q.1, P:Y.25

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: 3 residues within 4Å: Chain D: N.376, H.377, R.480 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 3 residues within 4Å: Chain E: N.376, H.377, R.480 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 3 residues within 4Å: Chain F: N.376, H.377, R.480 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-(1-3)-[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.25: 13 residues within 4Å: Chain F: T.248, N.250 Chain P: T.19, W.55, S.57, L.68, S.70, A.71, V.72, D.73, I.81, S.83, E.85 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:A.71 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.26: 13 residues within 4Å: Chain D: T.248, N.250 Chain R: T.19, W.55, S.57, L.68, S.70, A.71, V.72, D.73, I.81, S.83, E.85 1 PLIP interactions: 1 interactions with chain R Hydrogen bonds: R:A.71 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.27: 14 residues within 4Å: Chain E: T.248, N.250 Chain T: T.19, W.55, S.57, L.68, I.69, S.70, A.71, V.72, D.73, I.81, S.83, E.85 1 PLIP interactions: 1 interactions with chain T Hydrogen bonds: T:A.71

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

NAG.28: 2 residues within 4Å: Chain A: N.105, T.107 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: D.101, N.105 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: D.101, N.105 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain A: S.17 Chain D: G.92, N.93 Ligand excluded by PLIP NAG.32: 5 residues within 4Å: Chain D: E.309, N.311, I.348, S.349 Ligands: NAG-NAG.9 Ligand excluded by PLIP NAG.33: 7 residues within 4Å: Chain D: T.313, H.345, N.347, N.424, T.426 Ligands: NAG-NAG.9, NAG-NAG.9 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain D: K.350, N.354, W.409 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain D: N.370, K.371 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain D: P.403, N.406, T.419, G.420 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain D: N.410 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain D: R.268, N.278, A.307, N.459 Ligands: NAG-NAG-BMA-MAN-MAN.5 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: S.17 Chain E: G.92, N.93 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain E: E.309, N.311, I.348, S.349 Ligands: NAG-NAG.16 Ligand excluded by PLIP NAG.41: 7 residues within 4Å: Chain E: T.313, H.345, N.347, N.424, T.426 Ligands: NAG-NAG.16, NAG-NAG.16 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain E: K.350, N.354, W.409 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain E: N.370, K.371 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain E: P.403, N.406, T.419, G.420 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain E: N.410 Ligand excluded by PLIP NAG.46: 5 residues within 4Å: Chain E: R.268, N.278, A.307, N.459 Ligands: NAG-NAG-BMA-MAN-MAN.12 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain B: S.17 Chain F: G.92, N.93 Ligand excluded by PLIP NAG.48: 5 residues within 4Å: Chain F: E.309, N.311, I.348, S.349 Ligands: NAG-NAG.23 Ligand excluded by PLIP NAG.49: 7 residues within 4Å: Chain F: T.313, H.345, N.347, N.424, T.426 Ligands: NAG-NAG.23, NAG-NAG.23 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain F: K.350, N.354, W.409 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain F: N.370, K.371 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain F: P.403, N.406, T.419, G.420 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain F: N.410 Ligand excluded by PLIP NAG.54: 5 residues within 4Å: Chain F: R.268, N.278, A.307, N.459 Ligands: NAG-NAG-BMA-MAN-MAN.19 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, H. et al., Partially Open HIV-1 Envelope Structures Exhibit Conformational Changes Relevant for Coreceptor Binding and Fusion. Cell Host Microbe (2018)

Release Date

2018-10-17

Peptides

Envelope glycoprotein gp160: ABC
Envelope glycoprotein gp160: DEF
T-cell surface glycoprotein CD4: GHI
21c Fab VH domain: JLN
21c Fab VL domain: KMO
8ANC195 G52K5 Fab VH domain: PRT
8ANC195 G52K5 Fab VL domain: QSU

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

L
L

N
N

K
K

M
M

O
O

P
P

R
R

T
T

Q
Q

S
S

U
U

Envelope glycoprotein gp160

Envelope glycoprotein gp160

T-cell surface glycoprotein CD4

21c Fab VH domain

21c Fab VL domain

8ANC195 G52K5 Fab VH domain

8ANC195 G52K5 Fab VL domain

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