CRYSTAL STRUCTURES

Cancer-Related Protein Structures
HIV PR; Retroviral Protease Structures

Cancer-Related Protein Structures
Protein Significance PDB Code Resolution[Å]
Oxidase Group A Streptococcus HupZ 5ESC 2.0
Oxidase Wild type Nitronate Monooxygenase from Pseudomonas Aeruginosa PAO1 4Q4K 1.44
Oxidase Wild type Choline oxidase (pH=6.0) with the Reaction Product Glycine Betaine 4MJW 1.95
Oxidase Mutant S101A Choline oxidase 3NNE 2.48
Oxidase Mutant V464A Choline oxidase 3LJP 2.2
Enhanced Green Fluorescent Protein (EGFP) Calcium Sensor CatchER Ligand-Free 4L13 1.66
Enhanced Green Fluorescent Protein (EGFP) Calcium Sensor CatchER with Ca 4L11 1.20
Enhanced Green Fluorescent Protein (EGFP) Calcium Sensor CatchER with Gd 4L12 1.78
Dehydrogenase Pseudomonas aeruginosa D-Arginine Dehydrogenase 3NYC 1.06
Dehydrogenase Pseudomonas aeruginosa D-Arginine Dehydrogenase with Imino-Arginine 3NYE 1.30
Dehydrogenase Pseudomonas aeruginosa D-Arginine Dehydrogenase with Imino-Histidine 3NYF 1.30
Dehydrogenase Pseudomonas aeruginosa D-Arginine Dehydrogenase with an (N5) Flavin Adduct 3SM8 1.07
Caspase-3 Caspase-3 + Ac-D(ME)-Fmk 3GJR 2.2
Caspase-3 Caspase-3 + Ac-DEVD-Cho 2H5I 1.7
Caspase-3 Caspase-3 + Ac-DMQD-Cho 2H5J 2.0
Caspase-3 Caspase-3 + Ac-IEPD-Cho 3GJT 2.2
Caspase-3 Caspase-3 + Ac-LDESD-Cho 3EDQ 1.61
Caspase-3 Caspase-3 + Ac-VDVAD-Cho 2H65 2.3
Caspase-3 Caspase-3 + Ac-WEHD-Cho 3GJQ 2.6
Caspase-3 Caspase-3 + Ac-YVAD-Cho 3GJS 1.9
Caspase-7 Caspase-7 unliganded 3IBF 2.50
Caspase-7 Caspase-7 + Ac-DMQD-Cho 2QL5 2.34
Caspase-7 Caspase-7 + Ac-DNLD-Cho 2QLF 2.8
Caspase-7 Caspase-7 + Ac-DQMD-Cho 2QL9 2.14
Caspase-7 Caspase-7 + Ac-ESMD-Cho 2QLB 2.25
Caspase-7 Caspase-7 + Ac-IEPD-Cho 2QL7 2.4
Caspase-7 Caspase-7 + Ac-LDESD-Cho 3EDR 2.45
Caspase-7 Caspase-7 + Ac-WEHD-Cho 2QLJ 2.6
Caspase-7 Caspase-7 + Ac-YVAD-Cho 3IBC 2.75
SodA Bacillus subtilis superoxide dismutase 2RCV 1.6
Est30 carboxylesterase 30 with covalent reaction intermediate 1TQH 1.63
Est55 carboxylesterase 55 (pH=6.8) 2OGT 2.02
Est55 carboxylesterase 55 (pH=6.2) 2OGS 1.58
mTcl1 murine homolog of human oncoprotein 1JNP 2.50
MTCP1 human oncoprotein 1A1X 2.00
TNF-alpha
mutant R31D
1A8M 2.30
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HIV PR; Retroviral Protease Structures
Protein Significance PDB Code Resolution[Å]
HIV-1 PR
WT +  Amprenavir
3NU3 1.02
HIV-1 PR
mutant V32I +  Amprenavir
3NU4* 1.20
HIV-1 PR
mutant I50V +  Amprenavir
3NU5 1.29
HIV-1 PR
mutant I54M +  Amprenavir
3NU6* 1.16
HIV-1 PR
mutant I54V +  Amprenavir
3NUJ* 1.50
HIV-1 PR
mutant I84V +  Amprenavir
3NU9* 1.85
HIV-1 PR
mutant L90M +  Amprenavir
3NUO* 1.35
HIV-1 PR (Group N)
WT +  Darunavir
3MWS 1.09
HIV-1 PR
WT +  Darunavir (also called TMC-114 or UIC94017)
2IEN (replaces 1S6G) 1.30
HIV-1 PR
mutant D25N +  Darunavir
3BVB 1.30
HIV-1 PR
mutant D30N +  Darunavir
2F80 1.45
HIV-1 PR
mutant V32I +  Darunavir (Two Binding Sites)
2HS1 0.84
HIV-1 PR
mutant M46L +  Darunavir (Two Binding Sites)
2HS2 1.22
HIV-1 PR
mutant G48V +  Darunavir
3CYW 1.40
HIV-1 PR
mutant I50V +  Darunavir
2F8G 1.22
HIV-1 PR
mutant I54M +  Darunavir
3D1Z 1.30
HIV-1 PR
mutant I54V +  Darunavir
3D20 1.05
HIV-1 PR
mutant L76V +  Darunavir
3PWM 1.46
HIV-1 PR
mutant V82A +  Darunavir
2IDW* (replaces 1S65) 1.10
HIV-1 PR
mutant I84V +  Darunavir
2IEO (replaces 1S6S) 1.53
HIV-1 PR
mutant G86A +  Darunavir
3JVY 1.60
HIV-1 PR
mutant G86S +  Darunavir
3JW2 1.80
HIV-1 PR
mutant L90M +  Darunavir
2F81 1.25
HIV-1 PR
WT +  Indinavir
1SDT* 1.30
HIV-1 PR
mutant L24I +  Indinavir
2AVO* 1.10
HIV-1 PR
mutant I50V +  Indinavir
2AVS 1.10
HIV-1 PR
mutant G73S +  Indinavir (Spacegroup P21 with beta=98)
2AVV 1.50
HIV-1 PR
mutant V82A +  Indinavir
1SDV* 1.40
HIV-1 PR
mutant L90M +  Indinavir
1SDU* 1.25
HIV-1 PR
WT +  Saquinavir
3OXC (replaces 2NMW) 1.16
HIV-1 PR
mutant I50V +  Saquinavir
3CYX 1.20
HIV-1 PR
mutant I54M +  Saquinavir
3D1X 1.05
HIV-1 PR
mutant I54V +  Saquinavir
3D1Y* 1.05
HIV-1 PR
mutant L76V +  Saquinavir
3PWR 1.45
HIV-1 PR
mutant V82A +  Saquinavir (Spacegroup P21212)
2NMY 1.1
HIV-1 PR
mutant V82A +  Saquinavir (Spacegroup P212121)
2NMZ 0.97
HIV-1 PR
mutant I84V +  Saquinavir (Spacegroup P21212)
2NNK 1.25
HIV-1 PR
mutant I84V +  Saquinavir (Spacegroup P212121)
2NNP* 1.2
HIV-1 PR
WT +  GRL-98065
2Z4O 1.60
HIV-1 PR
mutant D30N +  GRL-98065
2QCI 1.20
HIV-1 PR
mutant I50V +  GRL-98065
2QD6 1.28
HIV-1 PR
mutant V82A +  GRL-98065
2QD7* 1.11
HIV-1 PR
mutant I84V +  GRL-98065
2QD8 1.35
HIV-1 PR
WT +  GRL-02031
3H5B 1.3
HIV-1 PR
mutant I47V +  GRL-02031
3VF5 1.25
HIV-1 PR
mutant L76V +  GRL-02031
3VF7* 1.3
HIV-1 PR
mutant V82A +  GRL-02031
3VFA 1.43
HIV-1 PR
mutant N88D +  GRL-02031
3VFB* 1.55
HIV-1 PR
WT +  GRL-0519A
3OK9 1.27
HIV-1 PR
mutant R8Q +  GRL-0519A
4HEG 1.46
HIV-1 PR
mutant D30N +  GRL-0519A
4HDB 1.49
HIV-1 PR
mutant I50V +  GRL-0519A
4HDP 1.22
HIV-1 PR
mutant I54M +  GRL-0519A
4HE9 1.06
HIV-1 PR
mutant V82A +  GRL-0519A
4HDF 1.29
HIV-1 PR
WT +  p2/NC (Spacegroup P212121)
1FGC* 1.90
HIV-1 PR
WT +  p2/NC (Spacegroup P21212)
2AOD* 1.40
HIV-1 PR
mutant L24I +  p2/NC
2AVM* 1.10
HIV-1 PR
mutant D25N +  p2/NC
3BVA* 1.05
HIV-1 PR
mutant D30N +  p2/NC
1FFI* 1.70
HIV-1 PR
mutant K45I +  p2/NC
1FF0* 1.85
HIV-1 PR
mutant I50V +  p2/NC
2AVQ* 1.30
HIV-1 PR
mutant V82A +  p2/NC
2AOG* 1.10
HIV-1 PR
mutant I84V +  p2/NC
2AOC* 1.30
HIV-1 PR
mutant N88D +  p2/NC
1FG6* 1.80
HIV-1 PR
mutant L90M +  p2/NC
1FEJ* 1.78
HIV-1 PR
WT +  p6/PR
2AOJ 1.60
HIV-1 PR
mutant V82A +  p6/PR
2AOH 1.42
HIV-1 PR
WT +  p1/p6
2AOI 1.38
HIV-1 PR
mutant V82A +  p1/p6
2AOF 1.32
HIV-1 PR
WT (triple mutant) +  CA/p2
1A8K* 2.00
HIV-1 PR
mutant R8Q  +  CA/p2 (Spacegroup P21)
1EBK* 2.06
HIV-1 PR
mutant D30N +  CA/p2
1FFF* 1.90
HIV-1 PR
mutant K43E +  CA/p2
1A94* 2.00
HIV-1 PR
mutant K45I +  CA/p2
1DAZ 1.55
HIV-1 PR
mutant V82A +  CA/p2
2AOE 1.54
HIV-1 PR
mutant N88D +  CA/p2
1FG8 1.85
HIV-1 PR
mutant L90M +  CA/p2
1DW6* 1.88
HIV-1 PR
mutant D30N, V82S +  CA/p2
1K2C* 2.20
HIV-1 PR
mutant K45I, V82S +  CA/p2
1K1T 1.20
HIV-1 PR
mutant K45I, L90M +  CA/p2
1K1U 1.55
HIV-1 PR
mutant N88D, L90M +  CA/p2
1K2B 1.70
HIV-1 PR
mutant V32I, I47V, V82I +  Amprenavir
3S43* 1.26
HIV-1 PR
mutant V32I, I47V, V82I +  Darunavir (Spacegroup P21212)
3S54 1.42
HIV-1 PR
mutant V32I, I47V, V82I +  Darunavir (Spacegroup P212121) (Two Binding Sites)
3S53* 1.50
HIV-1 PR
mutant V32I, I47V, V82I +  Saquinavir
3S56* 1.88
HIV-1 PR
S17 mutants +  No inhibitor
5T2E 1.50
HIV-1 PR
S17 mutants +  Darunavir
5T2Z 1.50
HIV-1 PR
mutant P51 (D25N) +  No inhibitor
4NPU 1.50
HIV-1 PR
mutant P51 (D25N) +  Darunavir
4NPT 1.66
HIV-1 PR
20 mutations +  YCl3
3UF3 1.65
HIV-1 PR
20 mutations +  Amprenavir (Two Binding Sites)
4J5J 1.80
HIV-1 PR
20 mutations +  Darunavir (Two Binding Sites)
3UCB 1.38
HIV-1 PR
20 mutations +  Saquinavir (Two Binding Sites)
3UFN* 1.45
HIV-1 PR
20 mutations +  GRL-02031 (Two Binding Sites)
4J55* 1.31
HIV-1 PR
20 mutations +  GRL-0519A (Two Binding Sites)
4J54* 1.55
HIV-1 PR
20 mutations +  GRL-044-10A
4YE3 1.35
HIV-1 PR
20 mutations +  GRL-050-10A
4HQ3 1.3
HIV-1 PR
20 mutations +  p2/NC
3UHL* 2.2
HIV-1 PR
20 mutations (D25N) (Tucked Flap)  
4Z50 1.45
HIV-1 PR
20 mutations (D25N) (Open Flap)  
4Z4X 1.75
HIV-1 PR
WT +  GRL-0105A
3DK1 1.07
HIV-1 PR
WT +  GRL-0255A
3DJK* 1.00
HIV-1 PR
WT +  GRL-0216A (macrocyclic inhibitor)
3I6O 1.17
HIV-1 PR
WT +  GRL-0518A (a isophthalamide-derived P2-P3 Ligand with the para-hydoxymethyl sulfonamide isostere as the P2' group)
5UPZ* 1.27
HIV-1 PR
WT +  GRL-0648A (a isophthalamide-derived P2-Ligand)
4ZIP 1.11
HIV-1 PR
WT +  GRL-1118A (a isophthalamide-derived P2-P3 Ligand with the sulfonamide isostere as the P2' group)
5UOV* 1.33
HIV-1 PR
WT +  GRL-0249A (Cyclopentyltetrahydro- furanyl Urethanes as P2-ligand)
4DFG 1.23
HIV-1 PR
WT +  GRL-0489A (C3-Substituted Hexahydrocyclopentafuranyl Urethane as P2-Ligand)
3ST5 1.45
HIV-1 PR
WT +  GRL-06579A
2HB3* 1.35
HIV-1 PR
WT +  GRL-0739A (tricyclic P2-ligands)
4KB9 1.29
HIV-1 PR
WT +  GRL-044-10A (a substituted bis-Tetrahydrofuran inhibitor)
3QAA 1.40
HIV-1 PR
WT +  GRL-050-10A (a Gem-difluoro-bis-Tetrahydrofuran as P2-Ligand)
4U8W 1.30
HIV-1 PR
WT +  GRL-004-11A (substituted fused-Tetrahydropyranyl Tetrahydrofuran as P2-Ligand)
5DGU 1.22
HIV-1 PR
WT +  GRL-011-11A (a methylamine bis-Tetrahydrofuran P2-Ligand, sulfonamide isostere derivate)
5BRY 1.34
HIV-1 PR
WT +  GRL-047-11A (a methylamine bis-Tetrahydrofuran P2-Ligand, 4-amino sulfonamide derivative)
5BS4 1.29
HIV-1 PR
WT +  GRL-105-11A (substituted fused-Tetrahydropyranyl Tetrahydrofuran as P2-Ligand)
5DGW 1.62
HIV-1 PR
WT +  GRL-096-13A (a Boc-derivative P2-Ligand, 3,-5-dimethylbiphenyl P1-Ligand)
4ZLS* 1.53
HIV-1 PR
WT +  GRL-100-13A (a Crown-like Oxotricyclic Core as the P2-Ligand with the sulfonamide isostere as the P2' group)
5ULT* 1.53
HIV-1 PR
WT +  GRL-097-13A (an Adamantane P1-Ligand with bis-THF in P2 and isobutylamine in P1')
5JFP* 1.49
HIV-1 PR
WT +  GRL-007-14A (an Adamantane P1-Ligand with bis-THF in P2 and benzylamine in P1')
5JFU* 1.70
HIV-1 PR
WT +  GRL-031-14A (an Adamantane P1-Ligand with tetrahydropyrano-tetrahydrofuran in P2 and isobutylamine in P1')
5JG1* 1.16
HIV-1 PR
mutant G86A +  DMP323
3JVW* 1.80
HIV-1 PR
WT +  intermediate
4FL8 1.20
HIV-1 PR
mutant V32I +  self proteolytic product
4FM6* 1.40
HIV-1 PR
mutant I47V +  self proteolytic product
4FLG 1.31
HIV-1 PR
WT +  self proteolytic product (with gem-diol-amine tetrahedral intermediate NLLTQI)
3B7V 1.46
HIV-1 PR
mutant I54V +  self proteolytic product (with gem-diol-amine tetrahedral intermediate NLLTQI)
3B80 1.50
HIV-1 PR
mutant F53L +  No inhibitor
2G69 1.35
Precursor HIV PR
WT +  Darunavir
3TKW 1.55
Precursor HIV PR
WT +  Saquinavir (2-dimer)
3TKG 1.36
Precursor HIV PR
WT +  Saquinavir
3TL9 1.32
HIV-2 PR
WT +  Amprenavir
3S45* 1.51
HIV-2 PR
WT +  Darunavir
3EBZ* 1.20
HIV-2 PR
WT +  GRL-98065
3ECG* 1.18
HIV-2 PR
WT +  GRL-06579A
3EC0* 1.18
RSV PR
engineered to recognize HIV-1 PR inhibitors + CA/p2
1BAI* 2.40
HIV-1 PR (Joint neutron and X-ray structure of per-deuterated)
WT +  Amprenavir
4JEC* 2.01
HIV-1 PR (Joint neutron and X-ray structure of per-deuterated)
mutant V32I, I47V, V82I +  Darunavir at pH 4.3
5E5K* 1.75
HIV-1 PR (Joint neutron and X-ray structure of per-deuterated)
mutant V32I, I47V, V82I +  Darunavir at pH 6.0
5E5J* 1.85
*: single orientation for the inhibitor or substrate analog
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