SMTL ID : 4flg.1

HIV-1 protease mutant I47V complexed with reaction intermediate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.31 Å

Oligo State

homo-dimer

Ligands

3 x ASP- GLN- ILE- ILE: HIV-1 protease, fragment(Non-covalent)

ASP-GLN-ILE-ILE.1: 23 residues within 4Å: Chain A: R.8, L.23, D.25, I.50, V.82 Chain B: D.25, G.27, A.28, D.29, D.30, K.45, V.47, G.48, G.49, I.50, I.84 Ligands: GLN-ILE-ILE.2, GLN-ILE-ILE.2, ILE-GLU-ILE.3, ILE-GLU-ILE.3, ILE-GLU-ILE.3, GLU.4, ILE.5 17 PLIP interactions: 5 interactions with chain A, 12 interactions with chain B Hydrophobic interactions: A:L.23, A:I.50, A:V.82, B:A.28, B:D.30, B:V.47, B:V.47, B:I.84 Hydrogen bonds: A:R.8, B:G.27, B:G.27, B:D.29, B:D.29, B:G.48, B:G.48 Water bridges: A:I.50, B:K.45 ASP-GLN-ILE-ILE.2: 21 residues within 4Å: Chain A: D.25, G.27, A.28, D.29, D.30, V.32, G.48, G.49, I.84 Chain B: R.8, L.23, D.25, I.50, V.82, I.84 Ligands: ASP-GLN-ILE-ILE.1, ASP-GLN-ILE-ILE.1, ILE-GLU-ILE.3, ILE-GLU-ILE.3, GLU.4, ILE.5 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:A.28, A:D.30, A:V.32, A:I.84, B:L.23, B:I.50, B:V.82, B:I.84 Hydrogen bonds: A:G.27, A:D.29, A:G.48, B:R.8 Water bridges: A:I.50 ASP-GLN-ILE-ILE.3: 21 residues within 4Å: Chain A: R.8, L.23, D.25, T.80, P.81, I.84 Chain B: G.27, A.28, D.29, D.30, V.47, G.48, G.49, I.50 Ligands: ASP-GLN-ILE-ILE.1, ASP-GLN-ILE-ILE.1, ASP-GLN-ILE-ILE.1, ASP-GLN-ILE-ILE.1, GLN-ILE-ILE.2, GLN-ILE-ILE.2, ILE.5 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:A.28, B:I.50, A:L.23, A:P.81, A:I.84 Hydrogen bonds: B:G.27, B:D.29, B:D.30, B:G.48, B:G.48, A:D.25

1 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.4: 13 residues within 4Å: Chain A: G.27, A.28, D.29, D.30, V.47, G.48, L.76 Chain B: I.50 Ligands: ASP-GLN-ILE-ILE.1, GLN-ILE-ILE.2, GLN-ILE-ILE.2, GLN-ILE-ILE.2, ILE.5 8 PLIP interactions: 4 interactions with chain A, 3 Ligand-Ligand interactions, 1 interactions with chain B Hydrogen bonds: A:G.27, A:D.29, A:D.30, A:D.30, E.4, E.4, E.4 Hydrophobic interactions: B:I.50

1 x ILE: ISOLEUCINE(Non-covalent)

ILE.5: 13 residues within 4Å: Chain A: G.27, G.49 Chain B: L.23, D.25, P.81, V.82, I.84 Ligands: ASP-GLN-ILE-ILE.1, GLN-ILE-ILE.2, GLN-ILE-ILE.2, GLN-ILE-ILE.2, ILE-GLU-ILE.3, GLU.4 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A, Hydrophobic interactions: B:L.23, B:P.81, B:V.82, B:I.84 Hydrogen bonds: B:D.25 Water bridges: A:I.50, A:I.50

1 x NA: SODIUM ION(Non-functional Binders)

NA.6: 1 residues within 4Å: Chain A: D.60 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.60, A:D.60

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 2 residues within 4Å: Chain A: R.41, W.42 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: K.14, G.16, G.17 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: T.91, A.95 Chain B: T.4, L.5 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain B: Q.2, I.3, T.4 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 4 residues within 4Å: Chain B: P.1, I.3, V.11, A.67 No protein-ligand interaction detected (PLIP) GOL.12: 6 residues within 4Å: Chain B: T.12, I.13, K.14, E.65, A.67, G.68 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.65, B:G.68 Water bridges: B:T.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shen, C.H. et al., Capturing the Reaction Pathway in Near-Atomic-Resolution Crystal Structures of HIV-1 Protease. Biochemistry (2012)

Release Date

2012-10-17

Peptides

HIV-1 protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

HIV-1 protease

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