eF-site ID 4yhz-HLP
PDB Code 4yhz
Chain H, L, P

click to enlarge
Title Crystal structure of 304M3-B Fab in complex with H3K4me3 peptide
Classification IMMUNE SYSTEM
Compound Fab Heavy Chain
Source (4YHZ)
Sequence H:  EVQLVETGGGVVQPGRSLRLSCTASGFTFRDYWMSWVRQA
PGKGLEWVADIHQDGQVRYYLDAVKGRFTISRDNAKSSLY
LQMNSLGAEDTAVYYCARNFVRGFGWHFDLWGRGTLVTVS
SASTKGPSVFPLAPSSGGTAALGCLVKDYFPEPVTVSWNS
GALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYIC
NVNHKPSNTKVDKKVEPKS
L:  LTQPPSVSVAPGQTARITCGGTNIGDISVHWYQQRPGQAP
LVVVYDDSDRPSGIPERFSGSNSGNTATLTISRVEAGDEA
DYYCQVWDDSINAYVFGTGTKVTVLRTVAAPSVFIFPPSD
SQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQES
VTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLS
SPVTKSFNRGE
P:  ARTXQTARK
Description (1)  Fab Heavy Chain, Fab Light Chain, H3K4me3 peptide


Functional site

1) chain H
residue 31
type
ligand
sequence D
description binding site for residue GOL H 301
source : AC1

2) chain H
residue 32
type
ligand
sequence Y
description binding site for residue GOL H 301
source : AC1

3) chain H
residue 53
type
ligand
sequence Q
description binding site for residue GOL H 301
source : AC1

4) chain H
residue 100
type
ligand
sequence F
description binding site for residue GOL H 301
source : AC1

5) chain H
residue 100
type
ligand
sequence F
description binding site for residue GOL H 301
source : AC1

6) chain H
residue 101
type
ligand
sequence V
description binding site for residue GOL H 301
source : AC1

7) chain H
residue 101
type
ligand
sequence V
description binding site for residue GOL H 301
source : AC1

8) chain H
residue 102
type
ligand
sequence R
description binding site for residue GOL H 301
source : AC1

9) chain H
residue 106
type
ligand
sequence W
description binding site for residue GOL H 301
source : AC1

10) chain H
residue 104
type
ligand
sequence F
description binding site for residue GOL H 302
source : AC2

11) chain H
residue 106
type
ligand
sequence W
description binding site for residue GOL H 302
source : AC2

12) chain H
residue 106
type
ligand
sequence W
description binding site for residue GOL H 302
source : AC2

13) chain P
residue 4
type
ligand
sequence X
description binding site for residue GOL H 302
source : AC2

14) chain P
residue 6
type
ligand
sequence T
description binding site for residue GOL H 302
source : AC2

15) chain H
residue 30
type
ligand
sequence R
description binding site for residue GOL H 303
source : AC3

16) chain H
residue 73
type
ligand
sequence D
description binding site for residue GOL H 303
source : AC3

17) chain H
residue 74
type
ligand
sequence N
description binding site for residue GOL H 303
source : AC3

18) chain H
residue 75
type
ligand
sequence A
description binding site for residue GOL H 303
source : AC3

19) chain H
residue 27
type
ligand
sequence F
description binding site for residue GOL H 304
source : AC4

20) chain H
residue 98
type
ligand
sequence R
description binding site for residue GOL H 304
source : AC4

21) chain H
residue 16
type
ligand
sequence R
description binding site for residue GOL H 305
source : AC5

22) chain H
residue 17
type
ligand
sequence S
description binding site for residue GOL H 305
source : AC5

23) chain L
residue 36
type
ligand
sequence Q
description binding site for residue GOL L 301
source : AC6

24) chain L
residue 38
type
ligand
sequence R
description binding site for residue GOL L 301
source : AC6

25) chain L
residue 57
type
ligand
sequence I
description binding site for residue GOL L 301
source : AC6

26) chain L
residue 58
type
ligand
sequence P
description binding site for residue GOL L 301
source : AC6

27) chain L
residue 61
type
ligand
sequence F
description binding site for residue GOL L 301
source : AC6

28) chain L
residue 80
type
ligand
sequence G
description binding site for residue GOL L 301
source : AC6

29) chain L
residue 81
type
ligand
sequence D
description binding site for residue GOL L 301
source : AC6

30) chain L
residue 58
type
ligand
sequence P
description binding site for residue GOL L 302
source : AC7

31) chain L
residue 59
type
ligand
sequence E
description binding site for residue GOL L 302
source : AC7

32) chain L
residue 60
type
ligand
sequence R
description binding site for residue GOL L 302
source : AC7

33) chain L
residue 76
type
ligand
sequence R
description binding site for residue GOL L 302
source : AC7

34) chain L
residue 67
type
ligand
sequence G
description binding site for residue SO4 L 303
source : AC8

35) chain L
residue 68
type
ligand
sequence N
description binding site for residue SO4 L 303
source : AC8

36) chain L
residue 69
type
ligand
sequence T
description binding site for residue SO4 L 303
source : AC8

37) chain H
residue 33
type
ligand
sequence W
description binding site for Ligand residues M3L P 4 through GLN P 5 bound to THR P 3
source : AC9

38) chain H
residue 50
type
ligand
sequence D
description binding site for Ligand residues M3L P 4 through GLN P 5 bound to THR P 3
source : AC9

39) chain H
residue 103
type
ligand
sequence G
description binding site for Ligand residues M3L P 4 through GLN P 5 bound to THR P 3
source : AC9

40) chain H
residue 106
type
ligand
sequence W
description binding site for Ligand residues M3L P 4 through GLN P 5 bound to THR P 3
source : AC9

41) chain L
residue 29
type
ligand
sequence D
description binding site for Ligand residues M3L P 4 through GLN P 5 bound to THR P 3
source : AC9

42) chain L
residue 90
type
ligand
sequence W
description binding site for Ligand residues M3L P 4 through GLN P 5 bound to THR P 3
source : AC9

43) chain L
residue 97
type
ligand
sequence Y
description binding site for Ligand residues M3L P 4 through GLN P 5 bound to THR P 3
source : AC9

44) chain P
residue 3
type
ligand
sequence T
description binding site for Ligand residues M3L P 4 through GLN P 5 bound to THR P 3
source : AC9

45) chain P
residue 6
type
ligand
sequence T
description binding site for Ligand residues M3L P 4 through GLN P 5 bound to THR P 3
source : AC9

46) chain P
residue 6
type
ligand
sequence T
description binding site for Ligand residues M3L P 4 through GLN P 5 bound to THR P 3
source : AC9

47) chain P
residue 7
type
ligand
sequence A
description binding site for Ligand residues M3L P 4 through GLN P 5 bound to THR P 3
source : AC9

48) chain H
residue 2
type binding
ligand GOL: GLYCEROL
sequence V
description GLYCEROL binding site
source pdb_hetatom : GOL_4yhz_H_304

49) chain H
residue 26-27
type binding
ligand GOL: GLYCEROL
sequence GF
description GLYCEROL binding site
source pdb_hetatom : GOL_4yhz_H_304

50) chain H
residue 32
type binding
ligand GOL: GLYCEROL
sequence Y
description GLYCEROL binding site
source pdb_hetatom : GOL_4yhz_H_304

51) chain H
residue 98
type binding
ligand GOL: GLYCEROL
sequence R
description GLYCEROL binding site
source pdb_hetatom : GOL_4yhz_H_304

52) chain H
residue 109
type binding
ligand GOL: GLYCEROL
sequence D
description GLYCEROL binding site
source pdb_hetatom : GOL_4yhz_H_304

53) chain H
residue 15-17
type binding
ligand GOL: GLYCEROL
sequence GRS
description GLYCEROL binding site
source pdb_hetatom : GOL_4yhz_H_305

54) chain H
residue 30
type binding
ligand GOL: GLYCEROL
sequence R
description GLYCEROL binding site
source pdb_hetatom : GOL_4yhz_H_303

55) chain H
residue 72-75
type binding
ligand GOL: GLYCEROL
sequence RDNA
description GLYCEROL binding site
source pdb_hetatom : GOL_4yhz_H_303

56) chain H
residue 31-33
type binding
ligand GOL: GLYCEROL
sequence DYW
description GLYCEROL binding site
source pdb_hetatom : GOL_4yhz_H_301

57) chain H
residue 53
type binding
ligand GOL: GLYCEROL
sequence Q
description GLYCEROL binding site
source pdb_hetatom : GOL_4yhz_H_301

58) chain H
residue 99-101
type binding
ligand GOL: GLYCEROL
sequence NFV
description GLYCEROL binding site
source pdb_hetatom : GOL_4yhz_H_301

59) chain H
residue 106
type binding
ligand GOL: GLYCEROL
sequence W
description GLYCEROL binding site
source pdb_hetatom : GOL_4yhz_H_301

60) chain H
residue 33
type binding
ligand M3L: N-TRIMETHYLLYSINE
sequence W
description N-TRIMETHYLLYSINE binding site
source pdb_hetatom : M3L_4yhz_P_4

61) chain H
residue 50
type binding
ligand M3L: N-TRIMETHYLLYSINE
sequence D
description N-TRIMETHYLLYSINE binding site
source pdb_hetatom : M3L_4yhz_P_4

62) chain H
residue 59
type binding
ligand M3L: N-TRIMETHYLLYSINE
sequence Y
description N-TRIMETHYLLYSINE binding site
source pdb_hetatom : M3L_4yhz_P_4

63) chain H
residue 99
type binding
ligand M3L: N-TRIMETHYLLYSINE
sequence N
description N-TRIMETHYLLYSINE binding site
source pdb_hetatom : M3L_4yhz_P_4

64) chain H
residue 106
type binding
ligand M3L: N-TRIMETHYLLYSINE
sequence W
description N-TRIMETHYLLYSINE binding site
source pdb_hetatom : M3L_4yhz_P_4

65) chain L
residue 90
type binding
ligand M3L: N-TRIMETHYLLYSINE
sequence W
description N-TRIMETHYLLYSINE binding site
source pdb_hetatom : M3L_4yhz_P_4

66) chain L
residue 97
type binding
ligand M3L: N-TRIMETHYLLYSINE
sequence Y
description N-TRIMETHYLLYSINE binding site
source pdb_hetatom : M3L_4yhz_P_4

67) chain P
residue 2-3
type binding
ligand M3L: N-TRIMETHYLLYSINE
sequence RT
description N-TRIMETHYLLYSINE binding site
source pdb_hetatom : M3L_4yhz_P_4

68) chain P
residue 5-6
type binding
ligand M3L: N-TRIMETHYLLYSINE
sequence QT
description N-TRIMETHYLLYSINE binding site
source pdb_hetatom : M3L_4yhz_P_4

69) chain H
residue 106
type binding
ligand GOL: GLYCEROL
sequence W
description GLYCEROL binding site
source pdb_hetatom : GOL_4yhz_H_302

70) chain P
residue 3
type binding
ligand GOL: GLYCEROL
sequence T
description GLYCEROL binding site
source pdb_hetatom : GOL_4yhz_H_302

71) chain P
residue 5-6
type binding
ligand GOL: GLYCEROL
sequence QT
description GLYCEROL binding site
source pdb_hetatom : GOL_4yhz_H_302

72) chain L
residue 36
type binding
ligand GOL: GLYCEROL
sequence Q
description GLYCEROL binding site
source pdb_hetatom : GOL_4yhz_L_301

73) chain L
residue 38
type binding
ligand GOL: GLYCEROL
sequence R
description GLYCEROL binding site
source pdb_hetatom : GOL_4yhz_L_301

74) chain L
residue 44
type binding
ligand GOL: GLYCEROL
sequence L
description GLYCEROL binding site
source pdb_hetatom : GOL_4yhz_L_301

75) chain L
residue 46
type binding
ligand GOL: GLYCEROL
sequence V
description GLYCEROL binding site
source pdb_hetatom : GOL_4yhz_L_301

76) chain L
residue 57-58
type binding
ligand GOL: GLYCEROL
sequence IP
description GLYCEROL binding site
source pdb_hetatom : GOL_4yhz_L_301

77) chain L
residue 60-61
type binding
ligand GOL: GLYCEROL
sequence RF
description GLYCEROL binding site
source pdb_hetatom : GOL_4yhz_L_301

78) chain L
residue 80-81
type binding
ligand GOL: GLYCEROL
sequence GD
description GLYCEROL binding site
source pdb_hetatom : GOL_4yhz_L_301

79) chain L
residue 85
type binding
ligand GOL: GLYCEROL
sequence Y
description GLYCEROL binding site
source pdb_hetatom : GOL_4yhz_L_301

80) chain L
residue 58-60
type binding
ligand GOL: GLYCEROL
sequence PER
description GLYCEROL binding site
source pdb_hetatom : GOL_4yhz_L_302

81) chain L
residue 76
type binding
ligand GOL: GLYCEROL
sequence R
description GLYCEROL binding site
source pdb_hetatom : GOL_4yhz_L_302


Display surface

Download
Links