SMTL ID : 6cm3.1

BG505 SOSIP in complex with sCD4, 17b, 8ANC195

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

6 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: 8 residues within 4Å: Chain A: 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: 8 residues within 4Å: Chain B: 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: 8 residues within 4Å: Chain C: 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.7: 3 residues within 4Å: Chain D: N.355, S.357 Ligands: NAG.19 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain E: N.355, S.357 Ligands: NAG.25 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain F: N.355, S.357 Ligands: NAG.31 No protein-ligand interaction detected (PLIP)

3 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-(1-6)-[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-MAN.4: 21 residues within 4Å: Chain D: K.202, N.204, H.321 Chain P: T.19, W.55, S.57, S.58, A.59, R.64, G.65, V.67, L.68, I.69, S.70, A.71, V.72, D.73, L.74, I.81, S.83, E.85 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:D.73, P:A.71 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.8: 21 residues within 4Å: Chain E: K.202, N.204 Chain R: T.19, T.29, W.55, S.57, S.58, A.59, R.64, G.65, V.67, L.68, I.69, S.70, A.71, V.72, D.73, L.74, I.81, S.83, E.85 1 PLIP interactions: 1 interactions with chain R Hydrogen bonds: R:D.73, R:A.71 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.12: 21 residues within 4Å: Chain F: K.202, N.204, H.321 Chain T: T.19, W.55, S.57, S.58, A.59, R.64, G.65, V.67, L.68, I.69, S.70, A.71, V.72, D.73, L.74, I.81, S.83, E.85 1 PLIP interactions: 1 interactions with chain T Hydrogen bonds: T:D.73, T:A.71

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: 13 residues within 4Å: Chain D: L.231, N.232, F.345, N.346, C.347, G.348, I.407, Q.408, G.409, R.412, V.414, S.415 Ligands: NAG.21 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.348, D:V.414, D:Q.408, D:Q.408, D:G.409 NAG-NAG-BMA-MAN-MAN.9: 13 residues within 4Å: Chain E: L.231, N.232, F.345, N.346, C.347, G.348, I.407, Q.408, G.409, R.412, V.414, S.415 Ligands: NAG.27 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:G.348, E:Q.408, E:Q.408, E:G.409 NAG-NAG-BMA-MAN-MAN.13: 13 residues within 4Å: Chain F: L.231, N.232, F.345, N.346, C.347, G.348, I.407, Q.408, G.409, R.412, V.414, S.415 Ligands: NAG.33 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:G.348, F:Q.408, F:Q.408, F:G.409

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: 7 residues within 4Å: Chain D: N.246, T.248, N.249 Chain P: H.3, Y.25, G.26, N.28 2 PLIP interactions: 2 interactions with chain P Hydrogen bonds: P:Q.1, P:Y.25, P:Y.25 NAG-NAG-BMA-MAN-MAN.10: 8 residues within 4Å: Chain E: N.246, T.248, N.249 Chain R: H.3, Y.25, G.26, V.27, N.28 2 PLIP interactions: 2 interactions with chain R Hydrogen bonds: R:Q.1, R:Y.25, R:Y.25 NAG-NAG-BMA-MAN-MAN.14: 7 residues within 4Å: Chain F: N.246, T.248, N.249 Chain T: H.3, Y.25, G.26, N.28 2 PLIP interactions: 2 interactions with chain T Hydrogen bonds: T:Q.1, T:Y.25, T:Y.25

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

NAG.16: 4 residues within 4Å: Chain D: N.265, S.303, R.412 Ligands: NAG.17 Ligand excluded by PLIP NAG.17: 5 residues within 4Å: Chain D: T.267, H.299, N.301, T.383 Ligands: NAG.16 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain D: N.308 Ligand excluded by PLIP NAG.19: 5 residues within 4Å: Chain D: N.332, S.333, T.341 Ligands: NAG-NAG.7, NAG-NAG.7 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain D: G.358, N.361 Ligand excluded by PLIP NAG.21: 5 residues within 4Å: Chain D: K.222, N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.5 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain E: N.265, S.303, R.412 Ligands: NAG.23 Ligand excluded by PLIP NAG.23: 5 residues within 4Å: Chain E: T.267, H.299, N.301, T.383 Ligands: NAG.22 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain E: N.308 Ligand excluded by PLIP NAG.25: 5 residues within 4Å: Chain E: N.332, S.333, T.341 Ligands: NAG-NAG.11, NAG-NAG.11 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain E: G.358, N.361 Ligand excluded by PLIP NAG.27: 6 residues within 4Å: Chain E: K.222, N.232, P.261, V.414, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.9 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain F: N.265, S.303, R.412 Ligands: NAG.29 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain F: T.267, H.299, N.301, T.383 Ligands: NAG.28 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain F: N.308 Ligand excluded by PLIP NAG.31: 5 residues within 4Å: Chain F: N.332, S.333, T.341 Ligands: NAG-NAG.15, NAG-NAG.15 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain F: G.358, N.361 Ligand excluded by PLIP NAG.33: 6 residues within 4Å: Chain F: K.222, N.232, P.261, V.414, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.13 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
17b Fab light chain: JLN
17b Fab heavy chain: KMO
8ANC195 Fab heavy chain: PRT
8ANC195 Fab light chain: 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

17b Fab light chain

17b Fab heavy chain

8ANC195 Fab heavy chain

8ANC195 Fab light chain

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