SMTL ID : 5i8h.1 (1 other biounit)

Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer in Complex with V3 Loop-targeting Antibody PGT122 Fab and Fusion Peptide-targeting Antibody VRC34.01 Fab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.30 Å

Oligo State

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

Ligands

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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-MAN-MAN.1: 7 residues within 4Å: Chain A: N.58 Chain B: G.16, S.17 Chain C: Y.102 Chain D: N.31, Y.50, S.67 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.31 NAG-NAG-BMA-MAN-MAN-MAN-MAN.23: 7 residues within 4Å: Chain G: N.58 Chain H: G.16, S.17 Chain I: Y.102 Chain J: N.31, Y.50, S.67 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:N.31 NAG-NAG-BMA-MAN-MAN-MAN-MAN.45: 7 residues within 4Å: Chain M: N.58 Chain N: G.16, S.17 Chain O: Y.102 Chain P: N.31, Y.50, S.67 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:N.31

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.2: 6 residues within 4Å: Chain A: V.104, T.105, N.118, S.120, Y.135 Chain F: R.91 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.24: 6 residues within 4Å: Chain G: V.104, T.105, N.118, S.120, Y.135 Chain L: R.91 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.46: 6 residues within 4Å: Chain M: V.104, T.105, N.118, S.120, Y.135 Chain R: R.91 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.3: 7 residues within 4Å: Chain A: T.98, Q.100, S.120, F.121, N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: V.144, R.162, N.167 Chain G: R.278 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.204, T.206, S.244, I.247 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain A: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 6 residues within 4Å: Chain A: N.332, S.333, S.357 Ligands: NAG-NAG.11, NAG-NAG.11, NAG-NAG.12 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain A: N.355, S.357 Ligands: NAG-NAG.10, NAG-NAG.10, NAG-NAG.12 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain A: N.361 Ligands: NAG-NAG.10, NAG-NAG.11 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 7 residues within 4Å: Chain G: T.98, Q.100, S.120, F.121, N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 4 residues within 4Å: Chain G: V.144, R.162, N.167 Chain M: R.278 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 4 residues within 4Å: Chain G: N.204, T.206, S.244, I.247 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 2 residues within 4Å: Chain G: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 6 residues within 4Å: Chain G: N.332, S.333, S.357 Ligands: NAG-NAG.33, NAG-NAG.33, NAG-NAG.34 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 5 residues within 4Å: Chain G: N.355, S.357 Ligands: NAG-NAG.32, NAG-NAG.32, NAG-NAG.34 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 3 residues within 4Å: Chain G: N.361 Ligands: NAG-NAG.32, NAG-NAG.33 No protein-ligand interaction detected (PLIP) NAG-NAG.47: 7 residues within 4Å: Chain M: T.98, Q.100, S.120, F.121, N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.48: 4 residues within 4Å: Chain A: R.278 Chain M: V.144, R.162, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.49: 4 residues within 4Å: Chain M: N.204, T.206, S.244, I.247 No protein-ligand interaction detected (PLIP) NAG-NAG.52: 2 residues within 4Å: Chain M: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.54: 6 residues within 4Å: Chain M: N.332, S.333, S.357 Ligands: NAG-NAG.55, NAG-NAG.55, NAG-NAG.56 No protein-ligand interaction detected (PLIP) NAG-NAG.55: 5 residues within 4Å: Chain M: N.355, S.357 Ligands: NAG-NAG.54, NAG-NAG.54, NAG-NAG.56 No protein-ligand interaction detected (PLIP) NAG-NAG.56: 3 residues within 4Å: Chain M: N.361 Ligands: NAG-NAG.54, NAG-NAG.55 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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.6: 13 residues within 4Å: Chain A: K.35, S.179, E.181, P.182, N.232, N.346, C.347, G.348, Q.408, C.413, V.414, S.415 Ligands: NAG-NAG-BMA.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.348 NAG-NAG-BMA-MAN-MAN-MAN.28: 13 residues within 4Å: Chain G: K.35, S.179, E.181, P.182, N.232, N.346, C.347, G.348, Q.408, C.413, V.414, S.415 Ligands: NAG-NAG-BMA.35 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:G.348 NAG-NAG-BMA-MAN-MAN-MAN.50: 13 residues within 4Å: Chain M: K.35, S.179, E.181, P.182, N.232, N.346, C.347, G.348, Q.408, C.413, V.414, S.415 Ligands: NAG-NAG-BMA.57 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:G.348

6 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: 7 residues within 4Å: Chain A: Q.263, N.265, N.301, S.303, S.381, R.412, V.414 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 4 residues within 4Å: Chain A: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.6 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.29: 7 residues within 4Å: Chain G: Q.263, N.265, N.301, S.303, S.381, R.412, V.414 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.35: 4 residues within 4Å: Chain G: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.28 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.51: 7 residues within 4Å: Chain M: Q.263, N.265, N.301, S.303, S.381, R.412, V.414 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.57: 4 residues within 4Å: Chain M: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.50 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-(1-3)-[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-MAN.9: 16 residues within 4Å: Chain A: T.267, R.296, H.299, N.301, D.380, T.383 Chain E: R.103, I.104, G.106, V.107 Chain F: N.44, N.45, N.46, P.60, G.61, S.62 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.296, A:R.296 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.31: 16 residues within 4Å: Chain G: T.267, R.296, H.299, N.301, D.380, T.383 Chain K: R.103, I.104, G.106, V.107 Chain L: N.44, N.45, N.46, P.60, G.61, S.62 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:R.296, G:R.296 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.53: 16 residues within 4Å: Chain M: T.267, R.296, H.299, N.301, D.380, T.383 Chain Q: R.103, I.104, G.106, V.107 Chain R: N.44, N.45, N.46, P.60, G.61, S.62 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:R.296, M:R.296

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.14: 11 residues within 4Å: Chain A: N.107, I.108 Chain E: Y.33, N.58, R.102, W.113, F.114, T.115 Chain F: W.88, D.89, T.94 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Y.33, E:Y.33, E:R.102, E:R.102, E:T.115 NAG-NAG-BMA-MAN.36: 11 residues within 4Å: Chain G: N.107, I.108 Chain K: Y.33, N.58, R.102, W.113, F.114, T.115 Chain L: W.88, D.89, T.94 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:Y.33, K:Y.33, K:R.102, K:R.102, K:T.115 NAG-NAG-BMA-MAN.58: 11 residues within 4Å: Chain M: N.107, I.108 Chain Q: Y.33, N.58, R.102, W.113, F.114, T.115 Chain R: W.88, D.89, T.94 1 PLIP interactions: 1 interactions with chain Q Hydrogen bonds: Q:Y.33, Q:Y.33, Q:R.102, Q:R.102, Q:T.115

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

NAG.15: 6 residues within 4Å: Chain A: T.102, N.103, D.110, R.113, K.117, K.159 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: N.246, T.248, N.249 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.324 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.308 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: N.100, S.102 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain B: N.107 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: E.123, N.126 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain E: S.7, T.21, N.23 Ligand excluded by PLIP NAG.37: 6 residues within 4Å: Chain G: T.102, N.103, D.110, R.113, K.117, K.159 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain G: N.246, T.248, N.249 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain G: N.324 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain G: N.308 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain H: N.100, S.102 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain H: N.107 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain H: E.123, N.126 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain K: S.7, T.21, N.23 Ligand excluded by PLIP NAG.59: 6 residues within 4Å: Chain M: T.102, N.103, D.110, R.113, K.117, K.159 Ligand excluded by PLIP NAG.60: 3 residues within 4Å: Chain M: N.246, T.248, N.249 Ligand excluded by PLIP NAG.61: 1 residues within 4Å: Chain M: N.324 Ligand excluded by PLIP NAG.62: 1 residues within 4Å: Chain M: N.308 Ligand excluded by PLIP NAG.63: 2 residues within 4Å: Chain N: N.100, S.102 Ligand excluded by PLIP NAG.64: 1 residues within 4Å: Chain N: N.107 Ligand excluded by PLIP NAG.65: 2 residues within 4Å: Chain N: E.123, N.126 Ligand excluded by PLIP NAG.66: 3 residues within 4Å: Chain Q: S.7, T.21, N.23 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kong, R. et al., Fusion peptide of HIV-1 as a site of vulnerability to neutralizing antibody. Science (2016)

Release Date

2016-05-25

Peptides

BG505 SOSIP.664 gp120: AGM
BG505 SOSIP.664 gp41: BHN
VRC34.01 Fab heavy chain: CIO
VRC34.01 Fab light chain: DJP
PGT122 Fab heavy chain: EKQ
PGT122 Fab light chain: FLR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

G
A

M
A

B
B

H
B

N
B

C
E

I
E

O
E

D
F

J
F

P
F

E
I

K
I

Q
I

F
J

L
J

R
J

BG505 SOSIP.664 gp120

BG505 SOSIP.664 gp41

VRC34.01 Fab heavy chain

VRC34.01 Fab light chain

PGT122 Fab heavy chain

PGT122 Fab light chain

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