SMTL ID : 6msy.1

Anti-HIV-1 Fab Fab 2G12 + Man4 re-refinement

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-2-2-mer

Ligands

2 x MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose

MAN-MAN-MAN-MAN.1: 13 residues within 4Å: Chain A: G.93, Y.94 Chain B: A.31, H.32, T.33, Y.57, K.99, G.100, L.104, S.105, D.106, N.107, D.108 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.31, B:T.33, B:T.33, B:D.108, B:D.108, B:D.108, A:G.93 MAN-MAN-MAN-MAN.7: 13 residues within 4Å: Chain C: G.93, Y.94 Chain D: A.31, H.32, T.33, Y.57, K.99, G.100, L.104, S.105, D.106, N.107, D.108 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:A.31, D:H.32, D:T.33, D:T.33, D:D.108, D:D.108, C:G.93

8 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.2: 1 residues within 4Å: Chain A: H.90 No protein-ligand interaction detected (PLIP) UNX.3: 1 residues within 4Å: Chain B: H.32 No protein-ligand interaction detected (PLIP) UNX.4: 1 residues within 4Å: Chain B: E.46 No protein-ligand interaction detected (PLIP) UNX.5: 4 residues within 4Å: Chain B: H.174 Chain C: N.138, D.167, D.170 No protein-ligand interaction detected (PLIP) UNX.8: 1 residues within 4Å: Chain C: H.90 No protein-ligand interaction detected (PLIP) UNX.9: 1 residues within 4Å: Chain D: H.32 No protein-ligand interaction detected (PLIP) UNX.10: 1 residues within 4Å: Chain D: E.46 No protein-ligand interaction detected (PLIP) UNX.11: 4 residues within 4Å: Chain A: N.138, D.167, D.170 Chain D: H.174 No protein-ligand interaction detected (PLIP)

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 3 residues within 4Å: Chain B: Y.57, R.58, D.59 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.57 ACT.12: 3 residues within 4Å: Chain D: Y.57, R.58, D.59 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Calarese, D.A. et al., Dissection of the carbohydrate specificity of the broadly neutralizing anti-HIV-1 antibody 2G12. Proc. Natl. Acad. Sci. U.S.A. (2005)

Release Date

2018-11-21

Peptides

Fab 2G12, light chain: AC
Fab 2g12, heavy chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

C
L

B
H

D
H

Fab 2G12, light chain

Fab 2g12, heavy chain

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