SMTL ID : 5i8h.2 (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: E.57, N.58 Chain C: Y.102 Chain D: S.17 Chain E: N.31, Y.50, S.67 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.22: 7 residues within 4Å: Chain G: E.57, N.58 Chain I: Y.102 Chain J: S.17 Chain K: N.31, Y.50, S.67 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.43: 7 residues within 4Å: Chain M: E.57, N.58 Chain O: Y.102 Chain P: S.17 Chain Q: N.31, Y.50, S.67 No protein-ligand interaction detected (PLIP)

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: 5 residues within 4Å: Chain A: V.104, T.105, N.118, S.120, Y.135 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.23: 5 residues within 4Å: Chain G: V.104, T.105, N.118, S.120, Y.135 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.44: 5 residues within 4Å: Chain M: V.104, T.105, N.118, S.120, Y.135 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)

NAG-NAG.3: 6 residues within 4Å: Chain A: T.98, Q.100, S.120, 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 M: 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.7: 5 residues within 4Å: Chain A: N.265, N.301, S.303, S.381, V.414 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-BMA.12 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain A: N.355, S.357 Ligands: NAG-NAG.10, NAG-NAG.10 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 6 residues within 4Å: Chain G: T.98, Q.100, S.120, N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 4 residues within 4Å: Chain A: R.278 Chain G: V.144, R.162, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 4 residues within 4Å: Chain G: N.204, T.206, S.244, I.247 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 5 residues within 4Å: Chain G: N.265, N.301, S.303, S.381, V.414 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 2 residues within 4Å: Chain G: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 6 residues within 4Å: Chain G: N.332, S.333, S.357 Ligands: NAG-NAG.32, NAG-NAG.32, NAG-NAG-BMA.33 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 4 residues within 4Å: Chain G: N.355, S.357 Ligands: NAG-NAG.31, NAG-NAG.31 No protein-ligand interaction detected (PLIP) NAG-NAG.45: 6 residues within 4Å: Chain M: T.98, Q.100, S.120, N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.46: 4 residues within 4Å: Chain G: R.278 Chain M: V.144, R.162, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.47: 4 residues within 4Å: Chain M: N.204, T.206, S.244, I.247 No protein-ligand interaction detected (PLIP) NAG-NAG.49: 5 residues within 4Å: Chain M: N.265, N.301, S.303, S.381, V.414 No protein-ligand interaction detected (PLIP) NAG-NAG.50: 2 residues within 4Å: Chain M: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.52: 6 residues within 4Å: Chain M: N.332, S.333, S.357 Ligands: NAG-NAG.53, NAG-NAG.53, NAG-NAG-BMA.54 No protein-ligand interaction detected (PLIP) NAG-NAG.53: 4 residues within 4Å: Chain M: N.355, S.357 Ligands: NAG-NAG.52, NAG-NAG.52 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: 12 residues within 4Å: Chain A: K.35, S.179, E.181, P.182, N.232, N.346, C.347, G.348, Q.408, 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.27: 12 residues within 4Å: Chain G: K.35, S.179, E.181, P.182, N.232, N.346, C.347, G.348, Q.408, V.414, S.415 Ligands: NAG-NAG-BMA.34 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:G.348 NAG-NAG-BMA-MAN-MAN-MAN.48: 12 residues within 4Å: Chain M: K.35, S.179, E.181, P.182, N.232, N.346, C.347, G.348, Q.408, V.414, S.415 Ligands: NAG-NAG-BMA.55 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:G.348

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: 17 residues within 4Å: Chain A: T.267, R.296, H.299, N.301, D.380, T.383 Chain B: S.24, N.44, N.45, N.46, P.60, G.61, S.62 Chain F: R.103, I.104, G.106, V.107 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.30: 17 residues within 4Å: Chain G: T.267, R.296, H.299, N.301, D.380, T.383 Chain H: S.24, N.44, N.45, N.46, P.60, G.61, S.62 Chain L: R.103, I.104, G.106, V.107 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.51: 17 residues within 4Å: Chain M: T.267, R.296, H.299, N.301, D.380, T.383 Chain N: S.24, N.44, N.45, N.46, P.60, G.61, S.62 Chain R: R.103, I.104, G.106, V.107 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:R.296, M:R.296

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.12: 2 residues within 4Å: Chain A: N.361 Ligands: NAG-NAG.10 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.33: 2 residues within 4Å: Chain G: N.361 Ligands: NAG-NAG.31 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.34: 4 residues within 4Å: Chain G: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.27 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.54: 2 residues within 4Å: Chain M: N.361 Ligands: NAG-NAG.52 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.55: 4 residues within 4Å: Chain M: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.48 No protein-ligand interaction detected (PLIP)

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

NAG.14: 4 residues within 4Å: Chain A: T.102, N.103, D.110, R.113 Ligand excluded by PLIP NAG.15: 8 residues within 4Å: Chain A: N.107, I.108 Chain B: W.88, D.89, R.92, T.94 Chain F: F.114, T.115 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.246, T.248 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 D: N.100, S.102 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain D: E.123, N.126 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain F: S.7, T.21, N.23 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain G: T.102, N.103, D.110, R.113 Ligand excluded by PLIP NAG.36: 8 residues within 4Å: Chain G: N.107, I.108 Chain H: W.88, D.89, R.92, T.94 Chain L: F.114, T.115 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain G: N.246, T.248 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain G: N.324 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain G: N.308 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain J: N.100, S.102 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain J: E.123, N.126 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain L: S.7, T.21, N.23 Ligand excluded by PLIP NAG.56: 4 residues within 4Å: Chain M: T.102, N.103, D.110, R.113 Ligand excluded by PLIP NAG.57: 8 residues within 4Å: Chain M: N.107, I.108 Chain N: W.88, D.89, R.92, T.94 Chain R: F.114, T.115 Ligand excluded by PLIP NAG.58: 2 residues within 4Å: Chain M: N.246, T.248 Ligand excluded by PLIP NAG.59: 1 residues within 4Å: Chain M: N.324 Ligand excluded by PLIP NAG.60: 1 residues within 4Å: Chain M: N.308 Ligand excluded by PLIP NAG.61: 2 residues within 4Å: Chain P: N.100, S.102 Ligand excluded by PLIP NAG.62: 2 residues within 4Å: Chain P: E.123, N.126 Ligand excluded by PLIP NAG.63: 3 residues within 4Å: Chain R: 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
PGT122 Fab light chain: BHN
VRC34.01 Fab heavy chain: CIO
BG505 SOSIP.664 gp41: DJP
VRC34.01 Fab light chain: EKQ
PGT122 Fab heavy chain: FLR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

G
C

M
C

B
L

H
L

N
L

C
G

I
G

O
G

D
D

J
D

P
D

E
H

K
H

Q
H

F
K

L
K

R
K

BG505 SOSIP.664 gp120

PGT122 Fab light chain

VRC34.01 Fab heavy chain

BG505 SOSIP.664 gp41

VRC34.01 Fab light chain

PGT122 Fab heavy chain

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